@article{stahr_lytle_avila_huseth_bertone_quesada-ocampo_2024, title={<i>Drosophila hydei</i> as a Potential Vector of <i>Ceratocystis fimbriata</i>, the Causal Agent of Sweetpotato Black Rot, in Storage Facilities}, volume={7}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-23-0328-R}, DOI={10.1094/PHYTO-09-23-0328-R}, abstractNote={, the causal agent of sweetpotato black rot, is a pathogen capable of developing and spreading within postharvest settings. A survey of North Carolina sweetpotato storage facilities was conducted to determine the arthropods present and identify potential vectors of}, journal={PHYTOPATHOLOGY}, author={Stahr, Madison and Lytle, Amanda and Avila, Kelly and Huseth, Anders S. and Bertone, Mathew and Quesada-Ocampo, Lina M.}, year={2024}, month={Jul} }
 @article{cochran_quesada-ocampo_kerns_thiessen_2024, title={<i>Phytophthora nicotianae</i>: A Quick Diagnostic Guide for Black Shank of Tobacco}, volume={5}, ISSN={["1535-1025"]}, url={https://doi.org/10.1094/PHP-10-23-0085-DG}, DOI={10.1094/PHP-10-23-0085-DG}, abstractNote={Phytophthora nicotianae is an oomycete pathogen that causes black shank of tobacco and is a major threat to tobacco production worldwide. P. nicotianae has been reported on 255 plant genera. Tobacco roots and crowns are the primary areas for disease symptoms but lower canopy leaf lesions can arise following initial infection. P. nicotianae can be isolated with semi-selective media from symptomatic tissue, contaminated water, and soil samples. The objective of this diagnostic guide is to provide a collection of current descriptions and methods for the symptomology, isolation, storage, and identification of P. nicotianae.}, journal={PLANT HEALTH PROGRESS}, author={Cochran, Sarah and Quesada-Ocampo, Lina M. and Kerns, James P. and Thiessen, Lindsey D.}, year={2024}, month={May} }
 @article{mascarenhas_quesada-ocampo_2024, title={Diagnostic Guide for Sclerotial Blight and Circular Spot of Sweetpotato}, volume={5}, ISSN={["1535-1025"]}, url={https://doi.org/10.1094/PHP-12-23-0110-DG}, DOI={10.1094/PHP-12-23-0110-DG}, abstractNote={Agroathelia rolfsii (anamorph: Sclerotium rolfsii) is a soilborne fungal pathogen that can cause disease on over 500 documented host species, including economically important field and vegetable crops. The pathogen commonly infects the stem or crown of most hosts, but it is also capable of damaging fruit and root structures that are near the soil line, resulting in wilting, stunting, and plant death. Two diseases caused by this pathogen are sclerotial blight and circular spot, both of which are detrimental for sweetpotato production. A. rolfsii is a necrotrophic pathogen and can be cultured from susceptible hosts and on artificial media. The purpose of this diagnostic guide is to provide characteristic traits for identifying A. rolfsii in sweetpotato as well as outline methods for pathogen isolation, morphological and molecular characterization, culture maintenance and long-term storage, and pathogenicity testing.}, journal={PLANT HEALTH PROGRESS}, author={Mascarenhas, J. and Quesada-Ocampo, L. M.}, year={2024}, month={May} }
 @article{shirley_vallad_quesada-ocampo_dufault_raid_2024, title={Effect of Cucurbit Host, Production Region, and Season on the Population Structure of <i>Pseudoperonospora cubensis</i> in Florida}, volume={2}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-12-22-2939-RE}, DOI={10.1094/PDIS-12-22-2939-RE}, abstractNote={ Pseudoperonospora cubensis, the causal agent of Cucurbit downy mildew (CDM), is one of the most important diseases affecting cucurbit production in the United States. This disease is especially damaging to Florida production areas, as the state is a top producer of many cucurbit species. In addition, winter production in central and south Florida likely serves as a likely source of P. cubensis inoculum for spring and summer cucurbit production throughout the eastern United States, where CDM is unable to overwinter in the absence of a living host. Over 2 years (2017 and 2018) and four seasons (spring 2017, spring 2018, fall 2017, and fall 2018), 274 P. cubensis isolates were collected from cucurbit hosts at production sites in south, central, and north Florida. The isolates were analyzed with 10 simple sequence repeat (SSR) markers to establish population structure and genetic diversity and further assigned to a clade based on a qPCR assay. Results of population structure and genetic diversity analyses differentiated isolates based on cucurbit host and clade (1 or 2). Of the isolates assigned to clade by qPCR, butternut squash, watermelon, and zucchini were dominated by clade 1 isolates, whereas cucumber isolates were split 34 and 59% between clades 1 and 2, respectively. Clade assignments agreed with isolate clustering observed within discriminant analysis of principal components (DAPC) based on SSR markers, although watermelon isolates formed a group distinct from the other clade 1 isolates. For seasonal collections from cucumber at each location, isolates were typically skewed to one clade or the other and varied across locations and seasons within each year of the study. This variable population structure of cucumber isolates could have consequences for regional disease management. This is the first study to characterize P. cubensis populations in Florida and evaluate the effect of cucurbit host and clade-type on isolate diversity and population structure, with implications for CDM management in Florida and other United States cucurbit production areas. }, journal={PLANT DISEASE}, author={Shirley, Andrew M. and Vallad, Gary E. and Quesada-Ocampo, Lina and Dufault, Nicholas and Raid, Richard}, year={2024}, month={Feb} }
 @article{parada-rojas_stahr_childs_quesada-ocampo_2024, title={Effector Repertoire of the Sweetpotato Black Rot Fungal Pathogen Ceratocystis fimbriata}, url={https://doi.org/10.1094/MPMI-09-23-0146-FI}, DOI={10.1094/MPMI-09-23-0146-FI}, abstractNote={ In 2015, sweetpotato producers in the United States experienced one of the worst outbreaks of black rot recorded in history, with up to 60% losses reported in the field and packing houses and at shipping ports. Host resistance remains the ideal management tool to decrease crop losses. Lack of knowledge of Ceratocystis fimbriata biology represents a critical barrier for the deployment of resistance to black rot in sweetpotato. In this study, we scanned the recent near chromosomal-level assembly for putative secreted effectors in the sweetpotato C. fimbriata isolate AS236 using a custom fungal effector annotation pipeline. We identified a set of 188 putative effectors on the basis of secretion signal and in silico prediction in EffectorP. We conducted a deep RNA time-course sequencing experiment to determine whether C. fimbriata modulates effectors in planta and to define a candidate list of effectors expressed during infection. We examined the expression profile of two C. fimbriata isolates, a pre-epidemic (1990s) isolate and a post-epidemic (2015) isolate. Our in planta expression profiling revealed clusters of co-expressed secreted effector candidates. Based on fold-change differences of putative effectors in both isolates and over the course of infection, we suggested prioritization of 31 effectors for functional characterization. Among this set, we identified several effectors that provide evidence for a marked biotrophic phase in C. fimbriata during infection of sweetpotato storage roots. Our study revealed a catalog of effector proteins that provide insight into C. fimbriata infection mechanisms and represent a core catalog to implement effector-assisted breeding in sweetpotato.  [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . }, journal={Molecular Plant-Microbe Interactions®}, author={Parada-Rojas, Camilo H. and Stahr, Madison and Childs, Kevin L. and Quesada-Ocampo, Lina M.}, year={2024}, month={Mar} }
 @article{stahr_parada-rojas_childs_alfenas_fernandes_avila_quesada-ocampo_2024, title={Long-Read Sequencing Genome Assembly of <i>Ceratocystis fimbriata</i> Enables Development of Molecular Diagnostics for Sweetpotato Black Rot}, volume={6}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-23-0341-R}, DOI={10.1094/PHYTO-09-23-0341-R}, abstractNote={is a destructive fungal pathogen of sweetpotato (}, journal={PHYTOPATHOLOGY}, author={Stahr, M. N. and Parada-Rojas, C. and Childs, K. L. and Alfenas, R. F. and Fernandes, F. M. and Avila, K. and Quesada-Ocampo, L. M.}, year={2024}, month={Jun} }
 @article{grunwald_bock_chang_de souza_del ponte_toit_dorrance_dung_gent_goss_et al._2024, title={Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices}, volume={4}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-12-23-0483-IA}, abstractNote={The landscape of scientific publishing is experiencing a transformative shift towards open access (OA), a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. OA provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in APS journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance is in line with those observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.}, journal={PHYTOPATHOLOGY}, author={Grunwald, Niklaus J. and Bock, Clive H. and Chang, Jeff H. and De Souza, Alessandra Alves and Del Ponte, Emerson M. and Toit, Lindsey J. and Dorrance, Anne E. and Dung, Jeremiah and Gent, David and Goss, Erica M. and et al.}, year={2024}, month={Apr} }
 @article{wong_quesada-ocampo_2024, title={Sensitivity of <i>Meloidogyne incognita</i>, <i>Fusarium oxysporum</i> f. sp. <i>niveum</i>, and <i>Stagonosporopsis citrulli</i> to Succinate Dehydrogenase Inhibitors Used for Control of Watermelon Diseases}, volume={5}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-12-22-2922-RE}, DOI={10.1094/PDIS-12-22-2922-RE}, abstractNote={Watermelon is affected by diseases such as Fusarium wilt, gummy stem blight, and root-knot nematode (RKN). Succinate dehydrogenase inhibitors (SDHIs) with potential fungicide and nematicide activity provide the opportunity to control multiple diseases with one compound. In this study, we aimed to determine the sensitivity of Meloidogyne incognita race 4 (MI4), Fusarium oxysporum f. sp. niveum (FON), and Stagonosporopsis citrulli (SCIT) to existing SDHIs: benzovindiflupyr, fluopyram, cyclobutrifluram, and pydiflumetofen. All SDHIs had fungicidal activity against 19 SCIT isolates in mycelial growth assays, but isolates were most sensitive to pydiflumetofen (median EC 50 = 0.41 μg/ml). Most of the 50 FON isolates tested were sensitive to cyclobutrifluram for mycelial growth (median EC 50 = 4.04 μg/ml) and conidial germination (median EC 50 = 0.2 μg/ml) assays but were not sensitive to fluopyram. MI4 was most sensitive to cyclobutrifluram for egg hatch (mean EC 50 = 0.0019 μg/ml) and J2 motility (mean EC 50 = 1.16 μg/ml) assays but was not sensitive to pydiflumetofen. Significant positive correlations between the sensitivity of SCIT (mycelial growth) and FON (mycelial growth and conidial germination) for cyclobutrifluram and benzovindiflupyr (SCIT r = 0.88; FON r = 0.7; P < 0.0001) and cyclobutrifluram and pydiflumetofen (SCIT r = 0.83; FON r = 0.67 and 0.77; P < 0.0001) indicate a potential for cross-resistance between these SDHIs for these fungal pathogens. Overall, results suggest that cyclobutrifluram may be used for managing RKN, whereas it should be used judiciously for Fusarium wilt of watermelon and gummy stem blight due to the existence of insensitive isolates to the fungicide.}, journal={PLANT DISEASE}, author={Wong, T. W. and Quesada-Ocampo, L. M.}, year={2024}, month={May} }
 @misc{quesada-ocampo_parada-rojas_hansen_vogel_smart_hausbeck_carmo_huitema_naegele_kousik_et al._2023, title={<i>Phytophthora capsici</i>: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description}, volume={61}, ISSN={["1545-2107"]}, DOI={10.1146/annurev-phyto-021622-103801}, abstractNote={ Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici. }, journal={ANNUAL REVIEW OF PHYTOPATHOLOGY}, author={Quesada-Ocampo, L. M. and Parada-Rojas, C. H. and Hansen, Z. and Vogel, G. and Smart, C. and Hausbeck, M. K. and Carmo, R. M. and Huitema, E. and Naegele, R. P. and Kousik, C. S. and et al.}, year={2023}, pages={185–208} }
 @article{d'arcangelo_wallace_miles_quesada-ocampo_2022, title={Carboxylic Acid Amide but Not Quinone Outside Inhibitor Fungicide Resistance Mutations Show Clade-Specific Occurrence in Pseudoperonospora cubensis Causing Downy Mildew in Commercial and Wild Cucurbits}, volume={8}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-05-22-0166-R}, DOI={10.1094/PHYTO-05-22-0166-R}, abstractNote={Since its reemergence in 2004, Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), has experienced significant changes in fungicide sensitivity. Presently, frequent fungicide applications are required to control the disease in cucumber due to the loss of host resistance. Carboxylic acid amides (CAA) and quinone outside inhibitors (QoI) are two fungicide groups used to control foliar diseases in cucurbits, including CDM. Resistance to these fungicides is associated with single nucleotide polymorphism (SNP) mutations. In this study, we used population analyses to determine the occurrence of fungicide resistance mutations to CAA and QoI fungicides in host-adapted clade 1 and clade 2 P. cubensis isolates. Our results revealed that CAA-resistant genotypes occurred more prominently in clade 2 isolates, with more sensitive genotypes observed in clade 1 isolates, while QoI resistance was widespread across isolates from both clades. We also determined that wild cucurbits can serve as reservoirs for P. cubensis isolates containing fungicide resistance alleles. Finally, we report that the G1105W substitution associated with CAA resistance was more prominent within clade 2 P. cubensis isolates while the G1105V resistance substitution and sensitivity genotypes were more prominent in clade 1 isolates. Our findings of clade-specific occurrence of fungicide resistance mutations highlight the importance of understanding the population dynamics of P. cubensis clades by crop and region to design effective fungicide programs and establish accurate baseline sensitivity to active ingredients in P. cubensis populations.}, journal={PHYTOPATHOLOGY}, author={D'Arcangelo, K. N. and Wallace, E. C. and Miles, T. D. and Quesada-Ocampo, L. M.}, year={2022}, month={Aug} }
 @article{sanogo_lamour_kousik_lozada_parada-rojas_quesada-ocampo_wyenandt_babadoost_hausbeck_hansen_et al._2022, title={Phytophthora capsici, 100 Years Later: Research Mile Markers from 1922 to 2022}, volume={11}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-08-22-0297-RVW}, DOI={10.1094/PHYTO-08-22-0297-RVW}, abstractNote={ In 1922, Phytophthora capsici was described by Leon Hatching Leonian as a new pathogen infecting pepper ( Capsicum annuum), with disease symptoms of root rot, stem and fruit blight, seed rot, and plant wilting and death. Extensive research has been conducted on P. capsici over the last 100 years. This review succinctly describes the salient mile markers of research on P. capsici with current perspectives on the pathogen's distribution, economic importance, epidemiology, genetics and genomics, fungicide resistance, host susceptibility, pathogenicity mechanisms, and management. }, journal={PHYTOPATHOLOGY}, author={Sanogo, Soum and Lamour, Kurt and Kousik, Chandrasekar S. and Lozada, Dennis N. and Parada-Rojas, Camilo H. and Quesada-Ocampo, Lina M. and Wyenandt, Christian A. and Babadoost, Mohammad and Hausbeck, Mary K. and Hansen, Zachariah and et al.}, year={2022}, month={Nov} }
 @misc{patel_quesada-ocampo_wehner_bhatta_correa_malla_2023, title={Recent Advances and Challenges in Management of Colletotrichum orbiculare, the Causal Agent of Watermelon Anthracnose}, volume={9}, ISSN={["2311-7524"]}, url={https://doi.org/10.3390/horticulturae9101132}, DOI={10.3390/horticulturae9101132}, abstractNote={The fungus Colletotrichum orbiculare causes watermelon anthracnose and is an important pathogen of watermelon in the United States, causing a significant impact on yield and quality of the produce. The application of fungicides as preventative and post-occurrence control measures is currently being deployed by growers. Further study of the genetic and molecular basis of anthracnose resistance will help in guiding future watermelon breeding strategies. Several conserved virulence factors (effectors) in C. orbiculare have been reported to interact with the host, at times impairing the host immune machinery. A single dominant gene conferring race 1 anthracnose resistance was reported independently on two watermelon germplasm. The recent advances in genomics, transcriptomics, proteomics, and metabolomics could facilitate a better understanding of the interaction between C. orbiculare effectors and host resistance genes in the already sequenced watermelon genome. In this review, we encompass and discuss (i) the history of watermelon anthracnose, taxonomy, morphology, and diversity in races of C. orbiculare; (ii) the epidemiology of the anthracnose disease and host resistance; (iii) the genetics behind the pathogenesis; and (iv) the current advances in breeding and molecular efforts to elucidate anthracnose resistance.}, number={10}, journal={HORTICULTURAE}, author={Patel, Takshay and Quesada-Ocampo, Lina M. and Wehner, Todd C. and Bhatta, Bed Prakash and Correa, Edgar and Malla, Subas}, year={2023}, month={Oct} }
 @article{bello_higgins_sakalidis_quesada-ocampo_martin_hausbeck_2022, title={Clade-Specific Monitoring of Airborne Pseudoperonospora spp. Sporangia Using Mitochondrial DNA Markers for Disease Management of Cucurbit Downy Mildew}, volume={112}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-12-21-0500-R}, DOI={10.1094/PHYTO-12-21-0500-R}, abstractNote={ Management of cucurbit downy mildew (CDM) caused by Pseudoperonospora cubensis, relies on an intensive fungicide program. In Michigan, CDM occurs annually due to an influx of airborne sporangia and timely alerts of airborne inoculum can assist growers in assessing the need to initiate fungicide sprays. This research aimed to improve the specific detection of airborne P. cubensis sporangia by adapting quantitative real-time polymerase chain reaction (qPCR) assays to distinguish among P. cubensis clades I and II and P. humuli in spore trap samples from commercial production sites and research plots. We also evaluated the suitability of impaction spore traps compared with Burkard traps for detection of airborne sporangia. A multiplex qPCR assay improved the specificity of P. cubensis clade II detection accelerating the assessment of field spore trap samples. After 2 years of monitoring, P. cubensis clade II DNA was detected in spore trap samples before CDM symptoms were first observed in cucumber fields (July and August), while P. cubensis clade I DNA was not detected in air samples before or after the disease onset. In some commercial cucumber fields, P. humuli DNA was detected throughout the growing season. The Burkard spore trap appeared to be better suited for recovery of sporangia at low concentrations than the impaction spore trap. This improved methodology for the monitoring of airborne Pseudoperonospora spp. sporangia could be used as part of a CDM risk advisory system to time fungicide applications that protect cucurbit crops in Michigan. }, number={10}, journal={PHYTOPATHOLOGY}, author={Bello, Julian C. and Higgins, Douglas S. and Sakalidis, Monique L. and Quesada-Ocampo, Lina M. and Martin, Frank and Hausbeck, Mary K.}, year={2022}, month={Oct}, pages={2110–2125} }
 @article{standish_gongora-castillo_bowman_childs_tian_quesada-ocampo_2022, title={Development, Validation, and Utility of Species-Specific Diagnostic Markers for Detection of Peronospora belbahrii}, volume={7}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-21-0393-R}, DOI={10.1094/PHYTO-09-21-0393-R}, abstractNote={ Peronospora belbahrii is an oomycete and the cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed; therefore, identifying P. belbahrii in seed lots before sale or planting or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next-generation sequencing reads for P. belbahrii, as well as publicly available DNA-seq and RNA-seq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict P. belbahrii-specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of P. belbahrii, host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used as templates to develop a highly sensitive probe-based real-time quantitative PCR (qPCR) assay that could detect P. belbahrii in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of P. belbahrii genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; P. belbahrii was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and identifying P. belbahrii-contaminated seed lots to mitigate the effects of future basil downy mildew epidemics. }, journal={PHYTOPATHOLOGY}, author={Standish, J. R. and Gongora-Castillo, E. and Bowman, M. J. and Childs, K. L. and Tian, M. and Quesada-Ocampo, L. M.}, year={2022}, month={Jul} }
 @article{shirley_vallad_dufault_raid_quesada-ocampo_2022, title={Duration of Downy Mildew Control Achieved with Fungicides on Cucumber Under Florida Field Conditions}, volume={106}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-03-21-0507-RE}, DOI={10.1094/PDIS-03-21-0507-RE}, abstractNote={ Cucurbit production in Florida is impacted by downy mildew on a yearly basis. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is one of the most devastating cucurbit diseases and can lead to complete yield loss. Nearly continuous production of cucurbits occurs temporally throughout Florida, which puts extensive pressure on the pathogen population to select for individuals that are resistant to fungicides in use labeled for CDM. Loss of efficacy as a result of fungicide resistance developing is becoming a major concern for Florida cucurbit growers who rely on these products to manage CDM. This study was established to evaluate the field activity of 11 utilized fungicides by determining their duration of activity when applied at various intervals for the management of CDM in cucumber under Florida field conditions. By comparing levels of percent CDM control and area under the disease progress curve values, the fungicide’s duration of field activity was established. Field activities were <1 week for dimethomorph and fluopicolide; 1 week for cymoxanil; 1 to 2 weeks for chlorothalonil and mancozeb; 2 weeks for ethaboxam; 1 to 3 weeks for propamocarb, cyazofamid, and ametoctradin + dimethomorph; and 2 to 4 weeks for oxathiapiprolin and fluazinam. Knowledge of duration of field activity can potentially improve the development of CDM management programs and slow the resistance selection. }, number={4}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Shirley, Andrew M. and Vallad, Gary E. and Dufault, Nicholas and Raid, Richard and Quesada-Ocampo, Lina}, year={2022}, month={Apr}, pages={1167–1174} }
 @article{parada-rojas_quesada-ocampo_2022, title={Phytophthora capsici Populations Are Structured by Host, Geography, and Fluopicolide Sensitivity}, volume={6}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-21-0403-R}, DOI={10.1094/PHYTO-09-21-0403-R}, abstractNote={ Phytophthora capsici epidemics are propelled by warm temperatures and wet conditions. With temperatures and inland flooding in many locations worldwide expected to rise as a result of global climate change, understanding of population structure can help to inform management of P. capsici in the field and prevent devastating epidemics. Thus, we investigated the effect of host crop, geographical origin, fungicide sensitivity, and mating type on shaping the population structure of P. capsici in the eastern United States. Our fungicide in vitro assays identified the emergence of insensitive isolates for fluopicolide and mefenoxam. A set of 12 microsatellite markers proved informative to assign 157 P. capsici isolates to five distinct genetic clusters. Implementation of Bayesian structure, population differentiation, genetic diversity statistics, and index of association analysis, allowed us to identify population structure by host with some correspondence with genetic clusters for cucumber and squash isolates. We found weak population structure by state for geographically close isolates. In this study, we discovered that North Carolina populations stratify by fluopicolide sensitivity with insensitive isolates experiencing nonrandom mating. Our findings highlight the need for careful monitoring of local field populations, improved selection of relevant isolates for breeding efforts, and hypervigilant surveillance of resistance to different fungicides. }, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Parada-Rojas, Camilo H. and Quesada-Ocampo, Lina M.}, year={2022}, month={Jun} }
 @article{wapshott-stehli_myers_quesada_grunden_stapelmann_2022, title={Plasma-driven biocatalysis: In situ hydrogen peroxide production with an atmospheric pressure plasma jet increases the performance of OleT(JE) when compared to adding the same molar amount of hydrogen peroxide in bolus}, volume={2}, ISSN={["1612-8869"]}, url={https://doi.org/10.1002/ppap.202100160}, DOI={10.1002/ppap.202100160}, abstractNote={AbstractEnzymes like fatty acid peroxygenase OleTJE are desirable enzymes for the industry. While they require inexpensive hydrogen peroxide for activity, the same hydrogen peroxide also causes overoxidation of their reactive heme center. Here, we generate hydrogen peroxide slowly in situ using the Cooperation in Science and Technology (COST)‐Jet, an atmospheric pressure plasma jet, to avoid overoxidizing OleTJE. The COST‐Jet was operated in helium with a water admixture to provide hydrogen peroxide for OleTJE activity. This helium/water admixture produced the highest enzyme turnover numbers after 2 min of treatment. These turnover numbers were even superior to using an equimolar amount of hydrogen peroxide to treat the enzymes exogenously, showing that this plasma source can provide a reliable amount of reaction mediator to support OleTJE activity.}, journal={PLASMA PROCESSES AND POLYMERS}, author={Wapshott-Stehli, Hannah L. and Myers, Brayden G. and Quesada, Maria J. Herrera and Grunden, Amy and Stapelmann, Katharina}, year={2022}, month={Feb} }
 @article{weldon_marks_gevens_kimberly n. d'arcangelo_quesada-ocampo_parry_gent_cadle-davidson_gadoury_2021, title={A Comprehensive Characterization of Ecological and Epidemiological Factors Driving Perennation of Podosphaera macularis Chasmothecia on Hop (Humulus lupulus)}, volume={111}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-11-20-0492-R}, DOI={10.1094/PHYTO-11-20-0492-R}, abstractNote={ Hop powdery mildew, caused by the ascomycete fungus Podosphaera macularis, is a consistent threat to sustainable hop production. The pathogen utilizes two reproductive strategies for overwintering and perennation: (i) asexual vegetative hyphae on dormant buds that emerge the following season as infected shoots; and (ii) sexual ascocarps (chasmothecia), which are discharged during spring rain events. We demonstrate that P. macularis chasmothecia, in the absence of any asexual P. macularis growth forms, are a viable overwintering source capable of causing early season infection two to three orders of magnitude greater than that reported for perennation via asexual growth. Two epidemiological models were defined that describe (i) temperature-driven maturation of P. macularis chasmothecia; and (ii) ascosporic discharge in response to duration of leaf wetness and prevailing temperatures. P. macularis ascospores were confirmed to be infectious at temperatures ranging from 5 to 20°C. The organism’s chasmothecia were also found to adhere tightly to the host tissue on which they formed, suggesting that these structures likely overwinter wherever hop tissue senesces within a hop yard. These observations suggest that existing early season disease management practices are especially crucial to controlling hop powdery mildew in the presence of P. macularis chasmothecia. Furthermore, these insights provide a baseline for the validation of weather-driven models describing maturation and release of P. macularis ascospores, models that can eventually be incorporated into hop disease management programs. }, number={11}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Weldon, William A. and Marks, Michelle E. and Gevens, Amanda J. and Kimberly N. D'Arcangelo and Quesada-Ocampo, Lina M. and Parry, Stephen and Gent, David H. and Cadle-Davidson, Lance E. and Gadoury, David M.}, year={2021}, month={Nov}, pages={1972–1982} }
 @article{parada-rojas_granke_naegele_hansen_hausbeck_kousik_mcgrath_smart_quesada-ocampo_2021, title={A Diagnostic Guide for Phytophthora capsici Infecting Vegetable Crops}, volume={22}, ISSN={["1535-1025"]}, url={https://doi.org/10.1094/PHP-02-21-0027-FI}, DOI={10.1094/PHP-02-21-0027-FI}, abstractNote={ Phytophthora capsici is an oomycete pathogen causing economically important diseases in a wide range of hosts worldwide including cucurbitaceous, solanaceous, and fabaceous crops. All plant parts, crown and roots, or only the fruit may be affected depending on the host, and symptoms can range from wilting to rot and plant death. Considered a hemibiotroph, P. capsici can be cultured in artificial media and maintained in long-term storage. In this diagnostic guide, we describe methods to identify P. capsici infection based on disease symptoms and pathogen signs. We also outline methods for molecular identification, pathogen isolation, storage of single-sporangium cultures, and pathogenicity testing. }, number={3}, journal={PLANT HEALTH PROGRESS}, publisher={Scientific Societies}, author={Parada-Rojas, Camilo H. and Granke, Leah L. and Naegele, Rachel P. and Hansen, Zachariah and Hausbeck, Mary K. and Kousik, Chandrasekar S. and McGrath, Margaret T. and Smart, Christine D. and Quesada-Ocampo, Lina M.}, year={2021}, pages={404–414} }
 @article{crandall_ramon_burkhardt_rodriguez_adair_gent_hausbeck_quesada-ocampo_martin_2021, title={A Multiplex TaqMan qPCR Assay for Detection and Quantification of Clade 1 and Clade 2 Isolates of Pseudoperonospora cubensis and Pseudoperonospora humuli}, volume={105}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-11-20-2339-RE}, DOI={10.1094/PDIS-11-20-2339-RE}, abstractNote={ The ability to detect and quantify aerially dispersed plant pathogens is essential for developing effective disease control measures and epidemiological models that optimize the timing for control. There is an acute need for managing the downy mildew pathogens infecting cucurbits and hop incited by members of the genus Pseudoperonospora (Pseudoperonospora cubensis clade 1 and 2 isolates and Pseudoperonospora humuli, respectively). A highly specific multiplex TaqMan quantitative polymerase chain reaction (PCR) assay targeting unique sequences in the pathogens’ mitochondrial genomes was developed that enables detection of all three taxa in a single multiplexed amplification. An internal control included in the reaction evaluated whether results were influenced by PCR inhibitors that can make it through the DNA extraction process. Reliable quantification of inoculum as low as three sporangia in a sample was observed. The multiplexed assay was tested with DNA extracted from purified sporangia, infected plant tissue, and environmental samples collected on impaction spore traps samplers. The ability to accurately detect and simultaneously quantify all three pathogens in a single multiplexed amplification should improve management options for controlling the diseases they cause. }, number={10}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Crandall, Sharifa G. and Ramon, Marina L. and Burkhardt, Alyssa K. and Rodriguez, Julian Camilo Bello and Adair, Nanci and Gent, David H. and Hausbeck, Mary K. and Quesada-Ocampo, Lina M. and Martin, Frank N.}, year={2021}, month={Oct}, pages={3154–3161} }
 @article{kimberly n. d'arcangelo_adams_kerns_quesada-ocampo_2021, title={Assessment of fungicide product applications and program approaches for control of downy mildew on pickling cucumber in North Carolina}, volume={140}, ISSN={["1873-6904"]}, url={https://doi.org/10.1016/j.cropro.2020.105412}, DOI={10.1016/j.cropro.2020.105412}, abstractNote={Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), is the most economically devastating and widespread disease of cucurbitaceous crops in the Eastern United States (US). Cucumbers are particularly susceptible and as a result, disease management of P. cubensis relies heavily on fungicide use. The re-emergence of P. cubensis in the US in 2004 resulted in the failure of previously effective host resistance and the pathogen has become less sensitive to several fungicides, limiting the efficacy of crop protection. The implementation of effective spray programs is recommended to minimize the development of fungicide resistance in pathogen populations. However, few studies have examined annual efficacy trials to generate robust recommendations. To determine the efficacy of fungicide applications on CDM in pickling cucumber regarding disease severity and marketable yield, field experiments were conducted from 2013 to 2016 in North Carolina. Evaluations included single-product fungicide applications as well as program treatments on susceptible cultivars. Although there was some variability between years due to differences in products applied, our analysis revealed that several single-site treatments were effective in the suppression of disease, including treatments that included oxathiapiprolin, cyazofamid, propamocarb, ethaboxam, fluazinam, and a mixture of mancozeb/zoxamide. Additionally, when compared to the non-treated controls, spray programs that included tank mixes with protectants and alternations of fungicide modes of action, resulted in lower levels of downy mildew and increased marketable yield.}, journal={CROP PROTECTION}, publisher={Elsevier BV}, author={Kimberly N. D'Arcangelo and Adams, Mike L. and Kerns, James P. and Quesada-Ocampo, Lina M.}, year={2021}, month={Feb} }
 @article{rahman_standish_d'arcangelo_quesada-ocampo_2021, title={Clade-Specific Biosurveillance of Pseudoperonospora cubensis Using Spore Traps for Precision Disease Management of Cucurbit Downy Mildew}, volume={111}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-06-20-0231-R}, DOI={10.1094/PHYTO-06-20-0231-R}, abstractNote={ Pseudoperonospora cubensis is an obligate oomycete and cause of cucurbit downy mildew (CDM), the most destructive foliar disease affecting cucurbit hosts. Annual epidemics develop throughout the United States as windborne sporangia travel great distances and survive prolonged exposure to solar radiation. Recent genomic evidence suggests that P. cubensis isolates display host adaptation based on their respective clade. Early detection is key for fungicide application timing, and identification of the host-adapted clade provides information on the risk of infection for specific cucurbit crops. In this study, a multiplex quantitative PCR assay was developed based on species- and clade-specific nuclear genomic markers. The assay detected as few as 10 sporangia or DNA at 100 fg/ml for both clades and was validated in the field by deploying rotorod spore samplers in cucurbit sentinel plots located at two research stations in North Carolina. Using this assay, sporangia DNA was detected in spore trap sampling rods before signs of P. cubensis or CDM symptoms were observed in the sentinel plots. Both clade 1 and clade 2 DNA were detected in late-season cucumber and watermelon plots but only clade 2 DNA was detected in the early-season cucumber plots. These results will significantly improve disease management of CDM by monitoring inoculum levels to determine the cucurbit crops at risk of infection throughout each growing season. }, number={2}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Rahman, A. and Standish, J. R. and D'Arcangelo, K. N. and Quesada-Ocampo, L. M.}, year={2021}, month={Feb}, pages={312–320} }
 @article{salcedo_al-haddad_buell_trail_góngora-castillo_quesada-ocampo_2021, title={Comparative Transcriptome Analysis of Two Contrasting Maize Inbred Lines Provides Insights on Molecular Mechanisms of Stalk Rot Resistance}, volume={10}, url={https://doi.org/10.1094/PHYTOFR-12-20-0055-R}, DOI={10.1094/PHYTOFR-12-20-0055-R}, abstractNote={ Maize stalk rot caused by Fusarium graminearum can lead to severe losses and accumulation of mycotoxins with detrimental effects on livestock health. Because few management strategies are available, the development of resistant varieties is considered the most cost-effective way to control the disease. However, the stalk-tissue-specific mechanisms underlying resistance to F. graminearum remain poorly understood, although it is believed to be strongly influenced by environmental factors. In this study, we performed a temporal transcriptome analysis of two maize inbred lines with contrasting responses to stalk rot using gene expression profiling. We observed differential downregulation of gene expression during the first 2 weeks in a resistant inbred line inoculated with F. graminearum. Time-course gene ontology enrichment analysis suggests that resistance may be caused by a modulation of gene expression associated with redox homeostasis, hormone biosynthesis, cytoskeleton activity, and cell wall remodeling. We validated our gene expression profiling data by measuring the expression of 10 differentially expressed genes using quantitative reverse-transcription PCR. Our analyses also revealed the effect of two environmental conditions with contrasting temperatures and relative humidity on the resistant phenotype and gene expression. This research expands our knowledge of molecular events underlying resistance to stalk rot and the effect of environmental conditions on the disease interaction. Our findings can be exploited for the development of resistant varieties.  [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . }, journal={PhytoFrontiers™}, publisher={Scientific Societies}, author={Salcedo, Andres and Al-Haddad, Jameel and Buell, C. Robin and Trail, Frances and Góngora-Castillo, Elsa and Quesada-Ocampo, Lina}, year={2021}, month={Dec} }
 @article{stahr_quesada-ocampo_2021, title={Effects of Water Temperature, Inoculum Concentration and Age, and Sanitizers on Infection of Ceratocystis fimbriata, Causal Agent of Black Rot in Sweetpotato}, volume={105}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-07-20-1475-RE}, DOI={10.1094/PDIS-07-20-1475-RE}, abstractNote={ Black rot, caused by Ceratocystis fimbriata, is a devastating postharvest disease of sweetpotato that recently re-emerged in 2014. Although the disease is known to develop in storage and during export to overseas markets, little is known as to how pathogen dispersal occurs. This study was designed to investigate dump tank water as a means of dispersal through four different types of water treatments: inoculum concentration (0, 5, 5 × 101, 5 × 102, and 5 × 103 spores/ml), inoculum age (0, 24, 48, 96, and 144 h), water temperature (10°C, 23°C, 35°C, and 45°C), and presence of a water sanitizer (DryTec, SaniDate, FruitGard, and Selectrocide). Wounded and nonwounded sweetpotato storage roots were soaked in each water treatment for 20 min, stored at 29°C for a 14-day period, and rated for disease incidence every other day. Disease was observed in sweetpotato storage roots in all water treatments tested, except in the negative controls. Disease incidence decreased with both inoculum concentration and inoculum age, yet values of 16.26% and up to 50% were observed for roots exposed to 5 spores/ml and 144-h water treatments, respectively. Sanitizer products that contained a form of chlorine as the active ingredient significantly reduced disease incidence in storage roots when compared with control roots and roots exposed to a hydrogen-peroxide based product. Finally, no significant differences in final incidence were detected in wounded sweetpotato storage roots exposed to water treatments of any temperature, but a significant reduction in disease progression was observed in the 45°C treatment. These findings indicate that if packing line dump tanks are improperly managed, they can aid C. fimbriata dispersal through the build-up of inoculum as infected roots are unknowingly washed after storage. Chlorine-based sanitizers can reduce infection when applied after root washing and not in the presence of high organic matter typically found in dump tanks. }, number={5}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Stahr, Madison N. and Quesada-Ocampo, Lina M.}, year={2021}, month={May}, pages={1365–1372} }
 @misc{salcedo_purayannur_standish_miles_thiessen_quesada-ocampo_2021, title={Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics}, volume={10}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants10030435}, DOI={10.3390/plants10030435}, abstractNote={Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.}, number={3}, journal={PLANTS-BASEL}, publisher={MDPI AG}, author={Salcedo, Andres F. and Purayannur, Savithri and Standish, Jeffrey R. and Miles, Timothy and Thiessen, Lindsey and Quesada-Ocampo, Lina M.}, year={2021}, month={Mar} }
 @article{purayannur_munster_bertone_quesada-ocampo_2021, title={First Report of Downy Mildew Caused by Peronospora chenopodii-ambrosioidis on Epazote (Dysphania ambrosioides) in North Carolina}, volume={22}, ISSN={["1535-1025"]}, url={https://doi.org/10.1094/PHP-12-20-0110-FI}, DOI={10.1094/PHP-12-20-0110-FI}, abstractNote={ In this brief, we report the observation of downy mildew caused by Peronospora chenopodii-ambrosioidis on epazote (Dysphania ambrosioides) in North Carolina, U.S.A. We performed morphological characterization of the sporangia and sporangiophores for identification. We also confirmed the identity of the pathogen by performing an alignment and generating a maximum likelihood phylogeny of the concatenated internal transcribed spacer region and cytochrome c oxidase subunit I sequences. }, number={3}, journal={PLANT HEALTH PROGRESS}, publisher={Scientific Societies}, author={Purayannur, Savithri and Munster, Michael J. and Bertone, Matthew A. and Quesada-Ocampo, Lina M.}, year={2021}, pages={384–386} }
 @article{kousik_quesada-ocampo_keinath_hausbeck_granke_naegele_ji_2021, title={Managing Stubborn Oomycete Plant Pathogens}, volume={22}, ISSN={["1535-1025"]}, url={https://doi.org/10.1094/PHP-08-21-0114-FI}, DOI={10.1094/PHP-08-21-0114-FI}, abstractNote={Diseases caused by oomycete plant pathogens result in devastating losses to agriculture and native forests, despite the significant research efforts that have advanced our understanding of these organisms. Limiting these pathogens has been challenging to plant pathologists and plant health practitioners. In this first focus issue , titled Managing Stubborn Oomycete Plant Pathogens, Plant Health Progress has assembled an array of manuscripts on the biology and management of Phytophthora, Pythium, Pseudoperonospora, Peronospora, and Aphanomyces spp. This focus issue has 28 peer-reviewed papers including three diagnostic guides, three mini-reviews, three briefs, two surveys, and 17 research papers. Of the 28 papers, 20 are on diseases caused by Phytophthora, four on Pythium, three on downy mildews, and one on Aphanomyces. All advance our understanding of these stubborn oomycete pathogens.}, number={3}, journal={PLANT HEALTH PROGRESS}, author={Kousik, Chandrasekar S. and Quesada-Ocampo, Lina M. and Keinath, Anthony and Hausbeck, Mary and Granke, Leah and Naegele, Rachel and Ji, Pingsheng}, year={2021}, pages={215–217} }
 @article{kousik_quesada-ocampo_keinath_hausbeck_granke_naegele_ji_2022, title={Managing Stubborn Oomycete Plant Pathogens Introduction}, volume={22}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-22-3}, abstractNote={Plant Health Progress Vol. 22 No. 3}, number={3}, journal={PLANT HEALTH PROGRESS}, author={Kousik, Chandrasekar S. and Quesada-Ocampo, Lina M. and Keinath, Anthony and Hausbeck, Mary and Granke, Leah and Naegele, Rachel and Ji, Pingsheng}, year={2022}, month={Jan}, pages={215–217} }
 @article{parada-rojas_pecota_almeyda_yencho_quesada-ocampo_2021, title={Sweetpotato Root Development Influences Susceptibility to Black Rot Caused by the Fungal Pathogen <i>Ceratocystis fimbriata}, volume={111}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-12-20-0541-R}, DOI={10.1094/PHYTO-12-20-0541-R}, abstractNote={ Black rot of sweetpotato, caused by Ceratocystis fimbriata, is an important reemerging disease threatening sweetpotato production in the United States. This study assessed disease susceptibility of the storage root surface, storage root cambium, and slips (vine cuttings) of 48 sweetpotato cultivars, advanced breeding lines, and wild relative accessions. We also characterized the effect of storage root development on susceptibility to C. fimbriata. None of the cultivars examined at the storage root level were resistant, with most cultivars exhibiting similar levels of susceptibility. In storage roots, Jewel and Covington were the least susceptible and significantly different from White Bonita, the most susceptible cultivar. In the slip, significant differences in disease incidence were observed for above- and below-ground plant structures among cultivars, advanced breeding lines, and wild relative accessions. Burgundy and Ipomoea littoralis displayed less below-ground disease incidence compared with NASPOT 8, Sunnyside, and LSU-417, the most susceptible cultivars. Correlation of black rot susceptibility between storage roots and slips was not significant, suggesting that slip assays are not useful to predict resistance in storage roots. Immature, early-developing storage roots were comparatively more susceptible than older, fully developed storage roots. The high significant correlation between the storage root cross-section area and the cross-sectional lesion ratio suggests the presence of an unfavorable environment for C. fimbriata as the storage root develops. Incorporating applications of effective fungicides at transplanting and during early-storage root development when sweetpotato tissues are most susceptible to black rot infection may improve disease management efforts. }, number={9}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Parada-Rojas, C. H. and Pecota, Kenneth and Almeyda, C. and Yencho, G. Craig and Quesada-Ocampo, L. M.}, year={2021}, month={Sep}, pages={1660–1669} }
 @article{purayannur_gent_miles_radisek_quesada-ocampo_2021, title={The hop downy mildew pathogen Pseudoperonospora humuli}, volume={5}, ISSN={["1364-3703"]}, url={https://doi.org/10.1111/mpp.13063}, DOI={10.1111/mpp.13063}, abstractNote={AbstractPseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew, one of the most devastating diseases of cultivated hop, Humulus lupulus. Downy mildew occurs in all production areas of the crop in the Northern Hemisphere and Argentina. The pathogen overwinters in hop crowns and roots, and causes considerable crop loss. Downy mildew is managed by sanitation practices, planting of resistant cultivars, and fungicide applications. However, the scarcity of sources of host resistance and fungicide resistance in pathogen populations complicates disease management. This review summarizes the current knowledge on the symptoms of the disease, life cycle, virulence factors, and management of hop downy mildew, including various forecasting systems available in the world. Additionally, recent developments in genomics and effector discovery, and the future prospects of using such resources in successful disease management are also discussed.TaxonomyClass: Oomycota; Order: Peronosporales; Family: Peronosporaceae; Genus: Pseudoperonospora; Species: Pseudoperonospora humuli.Disease symptomsThe disease is characterized by systemically infected chlorotic shoots called “spikes". Leaf symptoms and signs include angular chlorotic lesions and profuse sporulation on the abaxial side of the leaf. Under severe disease pressure, dark brown discolouration or lesions are observed on cones. Infected crowns have brown to black streaks when cut open. Cultivars highly susceptible to crown rot may die at this phase of the disease cycle without producing shoots. However, foliar symptoms may not be present on plants with systemically infected root systems.Infection processPathogen mycelium overwinters in buds and crowns, and emerges on infected shoots in spring. Profuse sporulation occurs on infected tissues and sporangia are released and dispersed by air currents. Under favourable conditions, sporangia germinate and produce biflagellate zoospores that infect healthy tissue, thus perpetuating the infection cycle. Though oospores are produced in infected tissues, their role in the infection cycle is not defined.ControlDowny mildew on hop is managed by a combination of sanitation practices and timely fungicide applications. Forecasting systems are used to time fungicide applications for successful management of the disease.Useful Websiteshttps://content.ces.ncsu.edu/hop‐downy‐mildew (North Carolina State University disease factsheet), https://www.canr.msu.edu/resources/michigan‐hop‐management‐guide (Michigan Hop Management Guide), http://uspest.org/risk/models (Oregon State University Integrated Plant Protection Center degree‐day model for hop downy mildew), https://www.usahops.org/cabinet/data/Field‐Guide.pdf (Field Guide for Integrated Pest Management in Hops).}, journal={MOLECULAR PLANT PATHOLOGY}, publisher={Wiley}, author={Purayannur, Savithri and Gent, David H. and Miles, Timothy D. and Radisek, Sebastjan and Quesada-Ocampo, Lina M.}, year={2021}, month={May} }
 @article{standish_raid_pigg_quesada-ocampo_2020, title={A Diagnostic Guide for Basil Downy Mildew}, volume={21}, url={https://doi.org/10.1094/PHP-09-19-0062-DG}, DOI={10.1094/PHP-09-19-0062-DG}, abstractNote={ Downy mildew, caused by the oomycete pathogen Peronospora belbahrii, is one of the most important diseases affecting sweet basil worldwide. Field- and greenhouse-grown basil may be affected, and crop losses are observed as the reduction of marketable leaves during both the production and postharvest handling stages. As an obligate biotroph, P. belbahrii cannot be cultured and maintained without live plant tissue, which may complicate efforts to diagnose and identify the causal agent. Thus, the goal of this diagnostic guide is to outline the appropriate methods required to identify basil downy mildew based on the symptoms of the disease and signs of the pathogen. Additionally, methods for pathogen identification, pathogen isolation, storage of single-sporangium cultures on live plants, and pathogenicity testing are described in detail. }, number={2}, journal={Plant Health Progress}, publisher={Scientific Societies}, author={Standish, Jeffrey R. and Raid, Richard N. and Pigg, Stacey and Quesada-Ocampo, Lina M.}, year={2020}, month={Jan}, pages={77–81} }
 @article{stahr_quesada-ocampo_2020, title={Assessing the Role of Temperature, Inoculum Density, and Wounding on Disease Progression of the Fungal Pathogen Ceratocystis fimbriata Causing Black Rot in Sweetpotato}, volume={104}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-12-18-2224-RE}, DOI={10.1094/PDIS-12-18-2224-RE}, abstractNote={ In 2014, Ceratocystis fimbriata, causal agent of black rot in sweetpotato, reemerged and inflicted large financial losses on growers in the United States. Black rot continues to damage sweetpotatoes and has become a priority to the industry since then. In contrast, little is known about the biology of C. fimbriata and the epidemiology of sweetpotato black rot. In this study, effects of environmental factors such as inoculum density, RH, and temperature on sweetpotato black rot were determined. Cured sweetpotatoes were wounded with a toothpick to simulate puncture wounds, inoculated with different spore suspensions (inoculum density) (104, 105, or 106 spores/ml), and incubated under different RH (85.53, 94.09, or 97.01%) and temperature (13, 18, 23, 29, or 35°C) for 21 days. In a separate experiment, five root wounding types (cuts, punctures, abrasions, end breaks, and macerating bruises) were compared. All wounded roots were subsequently soaked in a 103 spores/ml suspension and incubated at 100% RH and 23°C for 21 days. This study found 29 and 23°C to be the optimal temperature for black rot disease development and sporulation, respectively. No pathogen growth was observed at 13 and 35°C. Increased inoculum density significantly (P < 0.0001) increased disease incidence, but increasing RH had an effect only on sporulation area. All wound types resulted in increased disease incidence and sporulation as early as 7 days postinoculation. Our results highlight the importance of characterizing factors that affect disease development for achieving successful disease management strategies. Findings from this study will be used to improve disease management for sweetpotato black rot by suggesting tighter regulation of curing and storage conditions and better postharvest handling of sweetpotato roots to avoid unnecessary wounding. }, number={3}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Stahr, M. and Quesada-Ocampo, L. M.}, year={2020}, month={Mar}, pages={930–937} }
 @article{salcedo_hausbeck_pigg_quesada-ocampo_2020, title={Diagnostic Guide for Cucurbit Downy Mildew}, volume={21}, url={https://doi.org/10.1094/PHP-12-19-0095-DG}, DOI={10.1094/PHP-12-19-0095-DG}, abstractNote={ Cucurbit downy mildew caused by the oomycete Pseudoperonospora cubensis is the most devastating foliar disease on cultivated cucurbitaceous crops. Failure of host resistance in cucumber and previously effective fungicides has occurred in the last few years in the United States and Europe, making accurate and early diagnosis critical for timely disease management. The objective of this diagnostic guide is to describe the current taxonomy, host, geographic range, symptoms, and signs as well as effective techniques for pathogen identification, evaluation, isolation, and storage for P. cubensis. }, number={3}, journal={Plant Health Progress}, publisher={Scientific Societies}, author={Salcedo, Andres and Hausbeck, Mary and Pigg, Stacey and Quesada-Ocampo, Lina M.}, year={2020}, month={Jan}, pages={166–172} }
 @article{stahr_butler_huerta_ritchie_quesada-ocampo_2020, title={First Report of Bacterial Root Rot, Caused by Dickeya dadantii, on Sweetpotato (Ipomoea batatas) in North Carolina}, volume={104}, url={https://doi.org/10.1094/PDIS-03-20-0568-PDN}, DOI={10.1094/PDIS-03-20-0568-PDN}, abstractNote={HomePlant DiseaseVol. 104, No. 10First Report of Bacterial Root Rot, Caused by Dickeya dadantii, on Sweetpotato (Ipomoea batatas) in North Carolina PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Bacterial Root Rot, Caused by Dickeya dadantii, on Sweetpotato (Ipomoea batatas) in North CarolinaM. N. Stahr, S. Butler, A. I. Huerta, D. F. Ritchie, and L. M. Quesada-OcampoM. N. Stahr†Corresponding author: M. N. Stahr; E-mail Address: mnstahr@ncsu.eduhttp://orcid.org/0000-0001-6027-9611North Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695, S. ButlerNorth Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695Plant Disease and Insect Clinic, North Carolina State University, Raleigh, NC 27695, A. I. HuertaNorth Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695, D. F. RitchieNorth Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695, and L. M. Quesada-Ocampohttp://orcid.org/0000-0002-9072-7531North Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695AffiliationsAuthors and Affiliations M. N. Stahr1 † S. Butler1 2 A. I. Huerta1 D. F. Ritchie1 L. M. Quesada-Ocampo1 1North Carolina State University, Department of Entomology and Plant Pathology, Raleigh, NC 27695 2Plant Disease and Insect Clinic, North Carolina State University, Raleigh, NC 27695 Published Online:4 Aug 2020https://doi.org/10.1094/PDIS-03-20-0568-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat North Carolina (NC) produces over 50% of sweetpotatoes grown in the United States. In May of 2019, sweetpotato storage roots with soft rot symptoms from Johnston County, NC, were submitted to the NC State University Plant Disease and Insect Clinic (PDIC). The epidermis of some roots had light brown, water-soaked lesions with a dark black margin, and these roots also had internal rotted decay. Internal decay was also found in roots with no external symptoms. A gram-negative bacterium was isolated from symptomatic tissue. The colonies grew at 39°C and were small, off-white, circular, flat, and had smooth margins when grown on nutrient agar. Following the protocol of Stahr and Quesada-Ocampo (2020), five Covington variety storage roots were wounded with a toothpick and injected with 10 µl of a 107 CFU/ml suspension of isolated bacteria. Inoculated roots were stored without light at 29°C, and after 3 days they developed symptoms consistent with bacterial soft rot on the roots sent to the PDIC. The isolate was biochemically profiled using a BIOLOG GEN III MicroPlate and was found to utilize D-melibiose, raffinose, and mannitol, indicating Dickeya dianthicola (SIM 0.810) as the putative causal agent. To confirm BIOLOG results, DNA of the unknown isolate was extracted using a phenol-chloroform method (He 2011). Extracted DNA was screened using polymerase chain reaction (PCR) alongside a DNA panel of previously characterized strains of Dickeya dadantii, D. dianthicola, and Erwinia amylovora, Xanthomonas arboricola pv. pruni, and Pseudomonas syringae pv. syringae as outgroups, with diagnostic primers specific for the following: Dickeya and Pectobacterium spp. (Df-Dr, pelADE1-pelADE2, SR3F-SR1cR) (Laurila et al. 2010; Nassar et al. 1996; Toth et al. 1999); Pectobacterium carotovorum subsp. carotovorum (ExpccF-ExpccR) (Kang et al. 2003); P. atrosepticum (Y45-Y46) (Fréchon et al. 1998); and D. dianthicola (DIA-Cf-DIA-Cr and DDI-F1-DDI-R1) (Karim et al. 2019; Pritchard et al. 2013). Outgroup DNA failed to amplify in all reactions. The unknown isolate, D. dadantii and D. dianthicola, amplified a 130-, 150-, and 420-bp amplicon for the Df-Dr, SR3F-SR1cR, and pelADE1-pelADE2 primer sets, respectively, confirming the unknown isolate as Dickeya. The D. dianthicola primer set DIA-Cf and DIA-Cr amplified a 120-bp band only in the presence of D. dianthicola, contradicting the results of primer set DDI-F1-DDI-R1, for which the unknown isolate, D. dadantii and D dianthicola, amplified a positive 120-bp band. PCR amplicons of the unknown isolate were cleaned following the ExoSap-IT protocol, sequenced, and compared with the GenBank database using BLASTn. The Df-Dr (MT140883) and pelADE1-pelADE2 (MT140884) amplicons were 100 and 94.77% identical to D. dadantii strain DSM 18020 (CP023467.1), respectively. The DDI-F1-DDI-R1 amplicon (MT140886) was 99.37% identical to D. dadantii strain 3937 (CP002038.1), and the SR3F-SR1cR amplicon (MT140885) was 98.63% identical to the D. dadantii 16S ribosomal RNA gene (KX870942.1). From these results, the unknown isolate was determined to be D. dadantii, formerly known as E. chrysanthemi, which has not been previously reported on sweetpotato in NC. This pathogen was responsible for a severe epidemic that threatened the Georgia sweetpotato industry in the 1970s (Schaad and Brenner 1976); thus, more research is needed to evaluate the risk of a new epidemic occurring.The author(s) declare no conflict of interest.References:Fréchon, D., et al. 1998. Potato Res. 41:163. https://doi.org/10.1007/BF02358439 Crossref, ISI, Google ScholarHe, F. 2011. Bio Protoc. 101:e97. https://doi.org/10.21769/BioProtoc.97 Google ScholarKang, H. W., et al. 2003. Plant Pathol. 52:127. https://doi.org/10.1046/j.1365-3059.2003.00822.x Crossref, ISI, Google ScholarKarim, S., et al. 2019. Plant Dis. 103:2893. https://doi.org/10.1094/PDIS-10-18-1819-RE Link, ISI, Google ScholarLaurila, J., et al. 2010. Eur. J. Plant Pathol. 126:249. https://doi.org/10.1007/s10658-009-9537-9 Crossref, ISI, Google ScholarNassar, A., et al. 1996. Appl. Environ. Microbiol. 62:2228. https://doi.org/10.1128/AEM.62.7.2228-2235.1996 Crossref, ISI, Google ScholarPritchard, L., et al. 2013. Plant Pathol. 62:587. https://doi.org/10.1111/j.1365-3059.2012.02678.x Crossref, ISI, Google ScholarSchaad, N. W., and Brenner, D. 1976. Phytopathology 67:302. https://doi.org/10.1094/Phyto-67-302 ISI, Google ScholarStahr, M. N., and Quesada-Ocampo, L. M. 2020. Plant Dis. 104:930. https://doi.org/10.1094/PDIS-12-18-2224-RE Link, ISI, Google ScholarToth, I. K., et al. 1999. J. Appl. Microbiol. 87:770. https://doi.org/10.1046/j.1365-2672.1999.00929.x Crossref, ISI, Google ScholarThe author(s) declare no conflict of interest.Funding: Funding was provided by NC State Hatch Project (NC02628).DetailsFiguresLiterature CitedRelated Vol. 104, No. 10 October 2020SubscribeISSN:0191-2917e-ISSN:1943-7692 DownloadCaptionSymptoms of yellow leaf disease of Areca catechu caused by areca palm velarivirus 1 (H. X. Wang et al.). Photo credit: X. Huang. Fungal fruiting bodies of Phyllachora maydis on corn foliage resemble spots of tar (J. Valle-Torres et al.). Photo credit: C. Cruz. Geranium (Pelargonium hortorum) showing pale green and little leaves, phyllody, virescence, and witches’-broom (A. R. Amirmijani et al.). Photo credit: M. Azadvar. Metrics Article History Issue Date: 25 Sep 2020Published: 4 Aug 2020First Look: 5 May 2020Accepted: 4 May 2020 Pages: 2723-2723 Information© 2020 The American Phytopathological SocietyFundingNC State Hatch ProjectGrant/Award Number: NC02628Keywordsprokaryotesvegetablesepidemiologydisease development and spreadThe author(s) declare no conflict of interest.Cited bySweetpotato Root Development Influences Susceptibility to Black Rot Caused by the Fungal Pathogen Ceratocystis fimbriataC. H. Parada-Rojas, Kenneth Pecota, C. Almeyda, G. Craig Yencho, and L. M. Quesada-Ocampo3 October 2021 | Phytopathology®, Vol. 111, No. 9Effects of Water Temperature, Inoculum Concentration and Age, and Sanitizers on Infection of Ceratocystis fimbriata, Causal Agent of Black Rot in SweetpotatoMadison N. Stahr and Lina M. Quesada-Ocampo30 March 2021 | Plant Disease, Vol. 105, No. 5}, number={10}, journal={Plant Disease}, publisher={Scientific Societies}, author={Stahr, M. N. and Butler, S. and Huerta, A. I. and Ritchie, D. F. and Quesada-Ocampo, L. M.}, year={2020}, month={Oct}, pages={2723–2723} }
 @article{standish_sharpe_butler_quesada-ocampo_meadows_2020, title={First Report of Downy Mildew, Caused by Peronospora effusa, on Spinach (Spinacia oleracea) in North Carolina}, volume={21}, url={https://doi.org/10.1094/PHP-04-20-0025-BR}, DOI={10.1094/PHP-04-20-0025-BR}, abstractNote={ In this brief, we report the first observation of downy mildew caused by Peronospora effusa on spinach grown in North Carolina. To this end, we characterized the morphology of sporangiophores and sporangia, and compared the internal transcribed spacer region and cytochrome oxidase I sequences to confirm pathogen identity. }, number={3}, journal={Plant Health Progress}, publisher={Scientific Societies}, author={Standish, Jeffrey R. and Sharpe, Suzette and Butler, Shawn and Quesada-Ocampo, Lina M. and Meadows, Inga}, year={2020}, month={Jan}, pages={194–196} }
 @article{pastrana_cline_wong_watson_mercier_ivors_broome_quesada-ocampo_gordon_2020, title={First Report of Fusarium Wilt of Blackberry Caused by Fusarium oxysporum f. sp. mori in North Carolina}, volume={104}, url={https://doi.org/10.1094/PDIS-09-19-1980-PDN}, DOI={10.1094/PDIS-09-19-1980-PDN}, abstractNote={HomePlant DiseaseVol. 104, No. 3First Report of Fusarium Wilt of Blackberry Caused by Fusarium oxysporum f. sp. mori in North Carolina PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Fusarium Wilt of Blackberry Caused by Fusarium oxysporum f. sp. mori in North CarolinaA. M. Pastrana, W. O. Cline, T. W. Wong, D. C. Watson, J. Mercier, K. Ivors, J. C. Broome, L. M. Quesada-Ocampo, and T. R. GordonA. M. Pastranahttp://orcid.org/0000-0001-6540-4573University of California, Davis, CA 95616Search for more papers by this author, W. O. ClineNorth Carolina State University, Raleigh, NC 27695Search for more papers by this author, T. W. WongNorth Carolina State University, Raleigh, NC 27695Search for more papers by this author, D. C. WatsonUniversity of California, Davis, CA 95616Search for more papers by this author, J. MercierDriscoll’s Inc., Watsonville, CA 95076Search for more papers by this author, K. Ivorshttp://orcid.org/0000-0002-0930-3214Driscoll’s Inc., Watsonville, CA 95076Search for more papers by this author, J. C. BroomeDriscoll’s Inc., Watsonville, CA 95076Search for more papers by this author, L. M. Quesada-Ocampohttp://orcid.org/0000-0002-9072-7531North Carolina State University, Raleigh, NC 27695Search for more papers by this author, and T. R. Gordon†Corresponding author: T. R. Gordon; E-mail Address: trgordon@ucdavis.eduhttp://orcid.org/0000-0002-1715-6509University of California, Davis, CA 95616Search for more papers by this author AffiliationsAuthors and Affiliations A. M. Pastrana1 W. O. Cline2 T. W. Wong2 D. C. Watson1 J. Mercier3 K. Ivors3 J. C. Broome3 L. M. Quesada-Ocampo2 T. R. Gordon1 † 1University of California, Davis, CA 95616 2North Carolina State University, Raleigh, NC 27695 3Driscoll’s Inc., Watsonville, CA 95076 Published Online:22 Jan 2020https://doi.org/10.1094/PDIS-09-19-1980-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Beginning in 2015, wilting blackberry plants (Rubus L. subgenus Rubus) were observed in commercial plantings of cultivars BD467.1, BJ110.2, and Prime-Ark 45 in Pender County, North Carolina. Symptoms included chlorotic, wilted, or dried leaves on the entire cane. A dark, necrotic lesion on one side of the cane extending along the entire length of the cane was often visible. Complete or partial plant collapse was also observed, and up to 15% disease incidence occurred during fall 2018. Symptomatic blackberry plants of cultivar Prime-Ark 45 at one location in Pender County were sent to the North Carolina State University Plant Disease and Insect Clinic. To recover fungi from plants, infected tissues were surface sterilized in 1% NaOCl for 1 min. The tissue was rinsed in sterile distilled water, cut into small pieces, and placed on acidified potato dextrose agar (APDA). Two isolates, each from a different plant, were transferred from APDA to Nash and Snyder medium (Thies and Levi 2007), which is selective for Fusarium spp. Single strains (GL1963 and GL1964) were obtained by excising hyphal tips from recently germinated spores. Both isolates produced microconidia in false heads on short monophialides and macroconidia with elongated, bent apical cells and notched basal cells on carnation leaf agar, consistent with identification as Fusarium oxysporum Schlechtendahl emend. Snyder & Hansen (Leslie and Summerell 2006). Primer pairs iNL11/CNSa and iCNS11/NLa were used to amplify the intergenic spacer (O’Donnell et al. 2009). On the basis of a comparison of 2,281 bp, both isolates had identical sequences (GenBank accessions MN013360 and MN013361), which revealed a 100% match with sequences of F. oxysporum accessions in GenBank (AY527725.1) and Fusarium-ID (FD_00847_IGS) databases. A comparison with previously described blackberry isolates showed a 100% match with F. oxysporum f. sp. mori isolates from California (GenBank accessions KY515229 and KY515230). Complementary nit phenotypes obtained for each isolate, as described by Correll et al. (1987), were not compatible with F. oxysporum f. sp. mori strains previously identified in California. Both isolates from North Carolina were tested for pathogenicity to blackberry cultivar BJ110.2. For each isolate, five plants (approximately 8 months old) were inoculated by immersing roots for 10 min in a suspension of 5 × 106 spores/ml, which was obtained from cultures grown on PDA as described by Schmale and Gordon (2003). Thereafter, inoculated plants were placed in pots filled with Sunshine mix number 1 (SunGro Horticulture Canada). Each isolate was included in two independent pathogenicity tests, each of which included isolate GL1804 as the positive control (Pastrana et al. 2017). In each trial, five plants were immersed in sterile 0.1% water agar instead of a spore suspension to serve as negative controls. Inoculated and control plants were arranged in randomly assigned positions in a greenhouse with temperatures ranging from 15 to 30°C and relative humidity between 15 and 75%. By 6 to 7 weeks after inoculation, all inoculated plants were severely diseased or dead, and negative control plants remained healthy. F. oxysporum was recovered from stems and petioles of all symptomatic plants. This disease was previously reported in California and Mexico (Gordon et al. 2016; Hernandez-Cruz et al. 2015).The author(s) declare no conflict of interest.References:Correll, J. C., et al. 1987. Phytopathology 77:1640. https://doi.org/10.1094/Phyto-77-1640 Crossref, ISI, Google ScholarGordon, T. R., et al. 2016. Plant Dis. 100:1018. https://doi.org/10.1094/PDIS-07-15-0784-PDN Link, ISI, Google ScholarHernandez-Cruz, A., et al. 2015. Phytopathology 105:S4.59. Google ScholarLeslie, J. F., and Summerell, B. A. 2006. The Fusarium Laboratory Manual. Blackwell, Ames, IA. doi.org/10.1002/9780470278376 Crossref, Google ScholarO’Donnell, K., et al. 2009. Fungal Genet. Biol. 46:936. https://doi.org/10.1016/j.fgb.2009.08.006 Crossref, ISI, Google ScholarPastrana, A. M., et al. 2017. Plant Dis. 101:2066. https://doi.org/10.1094/PDIS-03-17-0428-RE Link, ISI, Google ScholarSchmale, D. G., and Gordon, T. R. 2003. Plant Pathol. 52:720. https://doi.org/10.1111/j.1365-3059.2003.00925.x Crossref, ISI, Google ScholarThies, J. A., and Levi, A. 2007. J. Nematol. 42:1530. Google ScholarThe author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 104, No. 3 March 2020SubscribeISSN:0191-2917e-ISSN:1943-7692 DownloadCaptionPathogenicity of Lasiodiploidia pseudotheobromae in a coffee plant 3 days after inoculation (R. L. Freitas-Lopes et al.). Photo credit: U. P. Lopes. Seedling blight of soybean caused by soilborne pathogens (J. R. Lamichhane et al.). Photo credit: M. I. Chilvers. Metrics Downloaded 2,444 times Article History Issue Date: 3 Mar 2020Published: 22 Jan 2020First Look: 10 Dec 2019Accepted: 6 Dec 2019 Page: 971 Information© 2020 The American Phytopathological SocietyKeywordsFusarium oxysporumblackberryNorth Carolinafirst reportThe author(s) declare no conflict of interest.Cited ByColonization of Wild Blackberry Plants in California by Fusarium oxysporum f. sp. moriAna M. Pastrana, Dean C. Watson, and Thomas R. Gordon1 January 2021 | Plant Disease, Vol. 105, No. 2}, number={3}, journal={Plant Disease}, publisher={Scientific Societies}, author={Pastrana, A. M. and Cline, W. O. and Wong, T. W. and Watson, D. C. and Mercier, J. and Ivors, K. and Broome, J. C. and Quesada-Ocampo, L. M. and Gordon, T. R.}, year={2020}, month={Mar}, pages={971} }
 @article{purayannur_miles_gent_pigg_quesada-ocampo_2020, title={Hop Downy Mildew Caused by Pseudoperonospora humuli: A Diagnostic Guide}, volume={21}, url={https://doi.org/10.1094/PHP-10-19-0072-DG}, DOI={10.1094/PHP-10-19-0072-DG}, abstractNote={ Downy mildew, caused by Pseudoperonospora humuli, is one of the most destructive diseases of hop. The purpose of this article is to provide an overview of the pathogen, the host range and geographical distribution, and the means to diagnose the disease. It is important to be able to diagnose downy mildew and distinguish it from other diseases for the timely application of suitable management practices. The procedures for laboratory propagation and maintenance of isolates are also presented. }, number={3}, journal={Plant Health Progress}, publisher={Scientific Societies}, author={Purayannur, Savithri and Miles, Timothy D. and Gent, David H. and Pigg, Stacey and Quesada-Ocampo, Lina M.}, year={2020}, month={Jan}, pages={173–179} }
 @article{wallace_d’arcangelo_quesada-ocampo_2020, title={Population Analyses Reveal Two Host-Adapted Clades of Pseudoperonospora cubensis, the Causal Agent of Cucurbit Downy Mildew, on Commercial and Wild Cucurbits}, volume={110}, url={https://doi.org/10.1094/PHYTO-01-20-0009-R}, DOI={10.1094/PHYTO-01-20-0009-R}, abstractNote={ Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is an airborne, obligate oomycete pathogen that re-emerged in 2004 and causes foliar disease and yield losses in all major cucurbit crops in the United States. Approximately 60 species in the family Cucurbitaceae have been reported as hosts of P. cubensis. Commercial hosts including cucumber, cantaloupe, pumpkin, squash, and watermelon are grown in North Carolina and many host species occur in the wild as weeds. Little is known about the contribution of wild cucurbits to the yearly epidemic; thus, this study aimed to determine the role of commercial and wild cucurbits in the structuring of P. cubensis populations in North Carolina, a region with high pathogen diversity. Ten microsatellite markers were used to analyze 385 isolates from six commercial and four wild cucurbits from three locations representing different growing regions across North Carolina. Population analyses revealed that wild and commercial cucurbits are hosts of P. cubensis in the United States, that host is the main factor structuring P. cubensis populations, and that P. cubensis has two distinct, host-adapted clades at the cucurbit species level, with clade 1 showing random mating and evidence of recombination and clade 2 showing nonrandom mating and no evidence of recombination. Our findings have implications for disease management because clade-specific factors such as host susceptibility and inoculum availability of each clade by region may influence P. cubensis outbreaks in different commercial cucurbits, timing of fungicide applications, and phenotyping for breeding efforts. }, number={9}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Wallace, E. C. and D’Arcangelo, K. N. and Quesada-Ocampo, L. M.}, year={2020}, month={Sep}, pages={1578–1587} }
 @article{miller_standish_quesada-ocampo_2020, title={Sensitivity of Fusarium oxysporum f. sp. niveum to Prothioconazole and Pydiflumetofen In Vitro and Efficacy for Fusarium Wilt Management in Watermelon}, volume={21}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-08-19-0056-RS}, abstractNote={ Field experiments were conducted in 2015 and 2016 to determine the effects of drench or drench-plus-foliar applications of prothioconazole and pydiflumetofen on Fusarium wilt (caused by Fusarium oxysporum f. sp. niveum; FON) of watermelon (Citrullus lanatus var. lanatus). In both years, all fungicide treatments reduced final disease incidence, final severity, and area under the disease progress curve, regardless of application rate or method. Yield data were collected in 2016, and both number and weight of marketable fruit were greatest in plots treated with pydiflumetofen as a drench-plus-foliar application at either application rate. Additional experiments were conducted to characterize sensitivity distributions of 48 isolates of FON from North Carolina to prothioconazole and pydiflumetofen. Mean prothioconazole EC50 values ranged from 0.10 to 0.55 µg/ml, and mean pydiflumetofen EC50 values ranged from 0.34 to 1.88 µg/ml. The results presented here validate pydiflumetofen as an effective management option for Fusarium wilt of watermelon, confirm previously observed efficacy of prothioconazole, and provide current evidence of pathogen sensitivity to these fungicides in North Carolina. }, number={1}, journal={PLANT HEALTH PROGRESS}, author={Miller, Nathan F. and Standish, Jeffrey R. and Quesada-Ocampo, Lina M.}, year={2020}, pages={13–18} }
 @article{grumet_fei_levi_mazourek_mccreight_schultheis_weng_hausbeck_kousik_ling_et al._2020, title={The CucCAP project: leveraging applied genomics to improve disease resistance in cucurbit crops}, volume={1294}, ISSN={["2406-6168"]}, DOI={10.17660/ActaHortic.2020.1294.12}, journal={VI INTERNATIONAL SYMPOSIUM ON CUCURBITS}, author={Grumet, R. and Fei, Z. and Levi, A. and Mazourek, M. and McCreight, J. D. and Schultheis, J. and Weng, Y. and Hausbeck, M. and Kousik, S. and Ling, K. S. and et al.}, year={2020}, pages={91–104} }
 @article{purayannur_cano_bowman_childs_gent_quesada-ocampo_2020, title={The Effector Repertoire of the Hop Downy Mildew Pathogen Pseudoperonospora humuli}, volume={11}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2020.00910}, abstractNote={Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew (DM), one of the most destructive diseases of cultivated hop that can lead to 100% crop loss in susceptible cultivars. We used the published genome of P. humuli to predict the secretome and effectorome and analyze the transcriptome variation among diverse isolates and during infection of hop leaves. Mining the predicted coding genes of the sequenced isolate OR502AA of P. humuli revealed a secretome of 1,250 genes. We identified 296 RXLR and RXLR-like effector-encoding genes in the secretome. Among the predicted RXLRs, there were several WY-motif-containing effectors that lacked canonical RXLR domains. Transcriptome analysis of sporangia from 12 different isolates collected from various hop cultivars revealed 754 secreted proteins and 201 RXLR effectors that showed transcript evidence across all isolates with reads per kilobase million (RPKM) values > 0. RNA-seq analysis of OR502AA-infected hop leaf samples at different time points after infection revealed highly expressed effectors that may play a relevant role in pathogenicity. Quantitative RT-PCR analysis confirmed the differential expression of selected effectors. We identified a set of P. humuli core effectors that showed transcript evidence in all tested isolates and elevated expression during infection. These effectors are ideal candidates for functional analysis and effector-assisted breeding to develop DM resistant hop cultivars.}, journal={FRONTIERS IN GENETICS}, author={Purayannur, Savithri and Cano, Liliana M. and Bowman, Megan J. and Childs, Kevin L. and Gent, David H. and Quesada-Ocampo, Lina M.}, year={2020}, month={Aug} }
 @article{baselga_schultheis_boyette_quesada-ocampo_starke_monks_2020, title={Vine Removal Prior to Harvest, and Curing Duration and Temperature Affect the Incidence and Severity of Internal Necrosis in 'Covington' Sweetpotato}, volume={30}, ISSN={["1943-7714"]}, DOI={10.21273/HORTTECH04408-19}, abstractNote={Internal necrosis (IN) is a physiological disorder that affects Covington, the most commonly grown sweetpotato (Ipomoea batatas) cultivar in North Carolina. Because IN affects the quality of sweetpotato storage roots, studies have been conducted since the first report of IN in 2006. Field studies (three in 2016 and two in 2017) were conducted to evaluate preharvest and postharvest treatments on the occurrence of IN in ‘Covington’ storage roots. Four preharvest treatments consisted of combinations of high chlorine or minimal chlorine potash fertilizer and mowing vs. not mowing before harvest. For postharvest treatments, 30 storage roots were obtained at harvest from each preharvest treatment plot and immediately cured in 75 and 85 °F rooms for a duration of 0.5, 1, 2, 3, and 5 weeks in 2016, and 0.5, 1, and 2 weeks in 2017. Shorter curing durations (0.5 and 1 week) coincided with industry recommendations while longer durations mimicked the challenges that some commercial facilities face when cooling down temperatures of rooms after curing is supposed to be concluded. Once curing temperature and curing duration treatments were completed, roots were placed in a 58 °F storage room at 85% relative humidity until cut. A control comparison was included in which harvested roots were placed in a 58 °F storage room (no curing) immediately after harvest. The storage roots from all temperature treatments were then cut 49 to 80 days after harvest, and incidence and severity of IN visually rated. Preharvest potash fertilizer treatments had minimal or no effect on occurrence of IN. However, mowing vines before harvest in several studies reduced IN incidence when roots were cured for more than 0.5 week at temperatures of at least 75 °F. Lower temperature (75 vs. 85 °F) and shorter curing duration (0.5 vs. 1, 2, 3, or 5 weeks) resulted in reduced IN occurrence in ‘Covington’ sweetpotato.}, number={5}, journal={HORTTECHNOLOGY}, author={Baselga, Fernando Montero de Espinosa and Schultheis, Jonathan R. and Boyette, Michael D. and Quesada-Ocampo, Lina M. and Starke, Keith D. and Monks, David W.}, year={2020}, month={Oct}, pages={544–551} }
 @article{stahr_quesada-ocampo_2019, title={Black Rot of Sweetpotato: A Comprehensive Diagnostic Guide}, volume={20}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-08-19-0052-DG}, abstractNote={ Black rot of sweetpotato (Ipomoea batatas) has been considered one of the most historically devastating diseases of the crop. The pathogen, Ceratocystis fimbriata (Ellis and Halst), is able to infect a variety of hosts including morning glory (Ipomoea sp.), coffee (Coffea sp.), and mango (Mangifera indica) over a wide geographic range. The slow-growing nature of the pathogen can lead to difficulty in isolating and maintaining cultures of the fungus. Thus, the objective for this diagnostic guide is to provide information about effective techniques for pathogen isolation, identification, storage, and pathogenicity testing as well as describe the host and geographic range, taxonomy, and disease in sweetpotato. }, number={4}, journal={PLANT HEALTH PROGRESS}, author={Stahr, Madison N. and Quesada-Ocampo, Lina M.}, year={2019}, pages={255–260} }
 @article{parada-rojas_quesada-ocampo_2019, title={Characterizing Sources of Resistance to Phytophthora Blight of Pepper Caused by Phytophthora capsici in North Carolina}, volume={20}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-09-18-0054-RS}, abstractNote={ Phytophthora blight, caused by Phytophthora capsici, is an important disease of peppers in the United States and worldwide. P. capsici causes crown, root, and fruit rot as well as foliar lesions in peppers. Field trials were conducted in 2015 and 2016 to evaluate 32 commercial and experimental pepper cultivars against a mixed-isolate inoculum in North Carolina. Cultivars Martha-R and Meeting were classified as highly resistant to P. capsici, and Paladin was classified as resistant. Intermediate resistance to P. capsici in the field was observed with Fabuloso, Revolution, Vanguard, Archimedes, Aristotle, Ebano-R, and Declaration. Greenhouse experiments were conducted to determine the response of 48 pepper cultivars when inoculated individually with two isolates from North Carolina and an isolate from Michigan. Isolates exhibited different levels of virulence in pepper cultivars screened for resistance. Landraces CM334 and Fidel as well as the cultivars Martha-R, Meeting, and Intruder were categorized as highly resistant or resistant to the three isolates tested. Overall, highly resistant cultivars tended to respond similarly to field mix inoculations and greenhouse single isolate inoculations. }, number={2}, journal={PLANT HEALTH PROGRESS}, author={Parada-Rojas, Camilo H. and Quesada-Ocampo, Lina M.}, year={2019}, pages={112–119} }
 @article{rahman_gongora-castillo_bowman_childs_gent_martin_quesada-ocampo_2019, title={Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection}, volume={109}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-11-18-0431-R}, DOI={10.1094/PHYTO-11-18-0431-R}, abstractNote={Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the Northern Hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur owing to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew. However, effective, sustainable, and cost-effective management of downy mildew can be improved by developing early detection systems to inform on disease risk and timely fungicide application. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of the P. humuli OR502AA isolate was partially sequenced using Illumina technology and assembled with ABySS. The assembly had a minimum scaffold length of 500 bp and an N50 (median scaffold length of the assembled genome) of 19.2 kbp. A total number of 18,656 genes were identified using MAKER standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using polymerase chain reaction against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in propagation material, such as rhizomes and vegetative cuttings, or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.}, number={8}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Rahman, A. and Gongora-Castillo, E. and Bowman, M. J. and Childs, K. L. and Gent, D. H. and Martin, F. N. and Quesada-Ocampo, L. M.}, year={2019}, month={Aug}, pages={1354–1366} }
 @article{munera_quesada-ocampo_rojas_chilvers_hausbeck_2019, title={Population Structure of Pythium ultimum from Greenhouse Floral Crops in Michigan}, volume={103}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-03-18-0394-RE}, DOI={10.1094/PDIS-03-18-0394-RE}, abstractNote={ Pythium ultimum causes seedling damping-off and root and crown rot in greenhouse ornamental plants. To understand the population dynamics and assess population structure of P. ultimum in Michigan floriculture crops, simple sequence repeats (SSRs) were developed using the previously published P. ultimum predicted transcriptome. A total of 166 isolates sampled from 2011 to 2013 from five, one, and three greenhouses in Kalamazoo, Kent, and Wayne Counties, respectively, were analyzed using six polymorphic and fluorescently labeled SSR markers. The average unbiased Simpson’s index (λu, 0.95), evenness (E5, 0.56), and recovery of 12 major clones out of the 65 multilocus genotypes obtained, suggests that P. ultimum is not a recent introduction into Michigan greenhouses. Analyses revealed a clonal population, with limited differentiation among seasons, hosts, and counties sampled. Results also indicated the presence of common genotypes among years, suggesting that sanitation measures should be enhanced to eradicate resident P. ultimum populations. Finally, the presence of common genotypes among counties suggests that there is an exchange of infected plant material among greenhouse facilities, or that there is a common source of inoculum coming to the region. Continued monitoring of pathogen populations will enhance our understanding of population dynamics of P. ultimum in Michigan and facilitate improvement of control strategies. }, number={5}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Munera, Johanna Del Castillo and Quesada-Ocampo, Lina M. and Rojas, Alejandro and Chilvers, Martin I. and Hausbeck, Mary K.}, year={2019}, month={May}, pages={859–867} }
 @article{crandall_rahman_quesada-ocampo_martin_bilodeau_miles_2018, title={Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges}, volume={102}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-09-17-1455-FE}, DOI={10.1094/pdis-09-17-1455-fe}, abstractNote={ Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States’ economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection. }, number={2}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Crandall, Sharifa G. and Rahman, Alamgir and Quesada-Ocampo, Lina M. and Martin, Frank N. and Bilodeau, Guillaume J. and Miles, Timothy D.}, year={2018}, month={Feb}, pages={265–275} }
 @article{parada-rojas_quesada-ocampo_2018, title={Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies}, volume={8}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-018-23438-8}, DOI={10.1038/s41598-018-23438-8}, abstractNote={AbstractPhytophthora capsici is a devastating oomycete that affects solanaceous, cucurbitaceous, fabaceous, and other crops in the United States (US) and worldwide. The release of the P. capsici genome allows for design of robust markers for genetic studies. We identified and characterized microsatellites in the P. capsici transcriptome. A subset of 50 microsatellites were assayed in a diverse set of P. capsici isolates and evaluated for polymorphism. Polymorphic microsatellites were confirmed by fragment analysis, and 12 were used for population characterization of 50 P. capsici isolates from different states, hosts, and mating types. Analysis of genetic relationship among isolates revealed significant geographic structure by state. Our findings highlight the usefulness of these 12 microsatellites to characterize the population structure of P. capsici and potential transferability to closely-related Phytophthora spp. since markers are located in coding regions. Our markers will facilitate genetic characterization and complement phenotypic studies of P. capsici populations, which may assist in deployment of disease management strategies.}, number={1}, journal={SCIENTIFIC REPORTS}, publisher={Springer Nature}, author={Parada-Rojas, C. H. and Quesada-Ocampo, L. M.}, year={2018}, month={Mar} }
 @article{wallace_quesada-ocampo_2017, title={Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseud operonospora populations}, volume={5}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.3266}, abstractNote={Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycetePseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in theP. cubensispredicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen,Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire ofP. cubensisto that of the model organismHyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified fromP. cubensistranscripts differed significantly fromH. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product inP. cubensisisolates, and 83 microsatellites demonstrated transferability toP. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified inP. cubensisisolates. Analysis ofPseudoperonosporaisolates from diverse hosts and locations revealed higher diversity inP. cubensiscompared toP. humuliisolates. These microsatellites will be useful in efforts to better understand relationships withinPseudoperonosporaspecies andP. cubensison a population level.}, journal={PEERJ}, author={Wallace, Emma C. and Quesada-Ocampo, Lina M.}, year={2017}, month={May} }
 @article{wallace_quesada-ocampo_2017, title={Examining the population structure of the cucurbit downy mildew pathogen, Pseudoperonospora cubensis, by host, location and time}, volume={107}, number={7}, journal={Phytopathology}, author={Wallace, E. and Quesada-Ocampo, L.}, year={2017}, pages={6–6} }
 @article{scruggs_basaiah_adams_quesada-ocampo_2017, title={Genetic Diversity, Fungicide Sensitivity, and Host Resistance to Ceratocystis fimbriata Infecting Sweetpotato in North Carolina}, volume={101}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-11-16-1583-re}, abstractNote={ Black rot of sweetpotato, caused by Ceratocystis fimbriata, has recently reemerged as a significant threat to sweetpotato production in North Carolina and other states across the United States. This disease has historically been controlled largely through cultural management strategies and, in some cases, fungicide application. The sudden and destructive reemergence of this disease in 2015 created the need for rapidly evaluating disease control strategies. Genetic diversity of current C. fimbriata isolates infecting sweetpotato in North Carolina was assessed using ITS, TEF, and MAT-2 sequences. All 50 tested isolates were confirmed to be of a single mating type, MAT-2, based on PCR amplification. Alignment of ITS, TEF, and MAT-2 sequences revealed all isolates were identical at each locus. Fourteen common sweetpotato cultivars and advanced breeding lines were screened for black rot resistance using two isolates. None of the cultivars were completely resistant to the disease and most were equally susceptible. ‘Stokes Purple’ and ‘Covington’ were the least susceptible, but significantly (P < 0.05) differed only from ‘Bellevue’, the most susceptible cultivar. Sensitivity of 50 C. fimbriata isolates to difenoconazole, fludioxonil, thiabendazole, dicloran, azoxystrobin, pyraclostrobin, fenamidone, and fluazinam was evaluated in vitro. Difenoconazole, thiabendazole, and fluazinam were most effective in reducing mycelia growth. Postharvest fungicide application on black rot-infected roots provided similar results. Low efficacy of dicloran, as well as a range of EC50 values among isolates, suggests potential resistance to this commonly applied fungicide. Results obtained in this study provide current and useful information so that improved recommendations can be made to reduce losses in sweetpotato to black rot. }, number={6}, journal={PLANT DISEASE}, author={Scruggs, A. C. and Basaiah, T. and Adams, M. L. and Quesada-Ocampo, L. M.}, year={2017}, month={Jun}, pages={994–1001} }
 @article{rahman_miles_martin_quesada-ocampo_2017, title={Molecular approaches for biosurveillance of the cucurbit downy mildew pathogen, Pseudoperonospora cubensis}, volume={39}, ISSN={["1715-2992"]}, url={https://doi.org/10.1080/07060661.2017.1357661}, DOI={10.1080/07060661.2017.1357661}, abstractNote={Abstract Globalization has allowed for rapid movement of plant pathogens that threaten food security. Successful disease management largely depends on timely and accurate detection of plant pathogens causing epidemics. Thus, biosurveillance of epidemic plant pathogens such as Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is becoming a priority to prevent disease outbreaks and deploy successful control efforts. Next Generation Sequencing (NGS) facilitates rapid development of genomics resources needed to generate molecular diagnostics assays for P. cubensis. Having information regarding the presence or absence of the pathogen, amount of inoculum, crop risk, time to initiate fungicide applications, and effective fungicides to apply would significantly contribute to reducing losses to cucurbit downy mildew. In this article, we discuss approaches to identify unique loci for rapid molecular diagnostics using genomic data, to develop molecular diagnostic tools that discriminate economically important pathogen alleles (i.e. mating type and fungicide resistance), and how to use molecular diagnostics with current and future spore trap strategies for biosurveillance purposes of important downy mildew pathogens. The combined use of these technologies within the already existent disease management framework has the potential to improve disease control.}, number={3}, journal={CANADIAN JOURNAL OF PLANT PATHOLOGY}, publisher={Informa UK Limited}, author={Rahman, Alamgir and Miles, Timothy D. and Martin, Frank N. and Quesada-Ocampo, Lina M.}, year={2017}, pages={282–296} }
 @article{thomas_carbone_choe_quesada-ocampo_ojiambo_2017, title={Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.3194}, DOI={10.1002/ece3.3194}, abstractNote={AbstractPseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), is known to exhibit host specialization. The virulence of different isolates of the pathogen can be classified into pathotypes based on their compatibility with a differential set composed of specific cucurbit host types. However, the genetic basis of host specialization within P. cubensis is not yet known. Total genomic DNA extracted from nine isolates of P. cubensis collected from 2008 to 2013 from diverse cucurbit host types (Cucumis sativus, C. melo var. reticulatus, Cucurbita maxima, C. moschata, C. pepo, and Citrullus lanatus) in the United States were subjected to whole‐genome sequencing. Comparative analysis of these nine genomes confirmed the presence of two distinct evolutionary lineages (lineages I and II) of P. cubensis. Many fixed polymorphisms separated lineage I comprising isolates from Cucurbita pepo, C. moschata, and Citrullus lanatus from lineage II comprising isolates from Cucumis spp. and Cucurbita maxima. Phenotypic characterization showed that lineage II isolates were of the A1 mating type and belonged to pathotypes 1 and 3 that were not known to be present in the United States prior to the resurgence of CDM in 2004. The association of lineage II isolates with the new pathotypes and a lack of genetic diversity among these isolates suggest that lineage II of P. cubensis is associated with the resurgence of CDM on cucumber in the United States.}, number={16}, journal={Ecology and Evolution}, publisher={Wiley}, author={Thomas, Anna and Carbone, Ignazio and Choe, Kisurb and Quesada-Ocampo, Lina M. and Ojiambo, Peter S.}, year={2017}, month={Jul}, pages={6231–6246} }
 @article{quesada-ocampo_2017, title={Using genomics approaches for rapid development of species-specific diagnostics for cucurbit downy mildew}, volume={39}, number={1}, journal={Canadian Journal of Plant Pathology}, author={Quesada-Ocampo, L.}, year={2017}, pages={106–106} }
 @article{scruggs_quesada-ocampo_2016, title={Cultural, Chemical, and Alternative Control Strategies for Rhizopus Soft Rot of Sweetpotato}, volume={100}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-01-16-0051-re}, abstractNote={ Rhizopus soft rot, caused primarily by Rhizopus stolonifer, is one of the most common postharvest diseases of sweetpotato and is often considered the most devastating. Traditionally, Rhizopus soft rot has been effectively controlled using postharvest dips in dicloran fungicides; however, due to changes in market preferences, use of these fungicides is now limited. This, along with the lack of labeled and effective fungicides for control of Rhizopus soft rot in sweetpotato, creates the need for integrated strategies to control the disease. The effects of storage temperature (13, 23, and 29°C), relative humidity (80, 90, and 100%), and initial inoculum levels (3-, 5-, and 7-mm-diameter mycelial plugs) on progression of Rhizopus soft rot in ‘Covington’ sweetpotato were examined. Percent decay due to Rhizopus soft rot infection was significantly reduced (P < 0.0001) at a low temperature (13°C) but was not significantly affected by changes in relative humidity or initial inoculum level (P >0.05). Sporulation of R. stolonifer was also significantly reduced at the lowest temperature of 13°C. High relative humidity (>95%) significantly increased sporulation of R. stolonifer and sporulation also increased as initial inoculum level increased. Efficacy of chlorine dioxide (ClO2) fumigation, UV-C irradiation, and postharvest dips in alternative control products were also investigated for control of Rhizopus soft rot. Static ClO2 treatments were effective in reducing sporulation on treated roots but had no significant impact on incidence of Rhizopus soft rot. UV irradiation at 3.24 KJ/m2 1 h after inoculation as well as dips in aqueous ClO2 and StorOx 2.0 significantly (P < 0.05) reduced disease incidence. Understanding the epidemiological factors favoring Rhizopus soft rot and identifying alternative control strategies allow for improved recommendations to limit postharvest losses in sweetpotato. }, number={8}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Scruggs, A. C. and Quesada-Ocampo, L. M.}, year={2016}, month={Aug}, pages={1532–1540} }
 @article{scruggs_quesada-ocampo_2016, title={Etiology and Epidemiological Conditions Promoting Fusarium Root Rot in Sweetpotato}, volume={106}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-01-16-0009-R}, DOI={10.1094/phyto-01-16-0009-r}, abstractNote={ Sweetpotato production in the United States is limited by several postharvest diseases, and one of the most common is Fusarium root rot. Although Fusarium solani is believed to be the primary causal agent of disease, numerous other Fusarium spp. have been reported to infect sweetpotato. However, the diversity of Fusarium spp. infecting sweetpotato in North Carolina is unknown. In addition, the lack of labeled and effective fungicides for control of Fusarium root rot in sweetpotato creates the need for integrated strategies to control disease. Nonetheless, epidemiological factors that promote Fusarium root rot in sweetpotato remain unexplored. A survey of Fusarium spp. infecting sweetpotato in North Carolina identified six species contributing to disease, with F. solani as the primary causal agent. The effects of storage temperature (13, 18, 23, 29, and 35°C), relative humidity (80, 90, and 100%), and initial inoculum level (3-, 5-, and 7-mm-diameter mycelia plug) were examined for progression of Fusarium root rot caused by F. solani and F. proliferatum on ‘Covington’ sweetpotato. Fusarium root rot was significantly reduced (P < 0.05) at lower temperatures (13°C), low relative humidity levels (80%), and low initial inoculum levels for both pathogens. Sporulation of F. proliferatum was also reduced under the same conditions. Qualitative mycotoxin analysis of roots infected with one of five Fusarium spp. revealed the production of fumonisin B1 by F. proliferatum when infecting sweetpotato. This study is a step toward characterizing the etiology and epidemiology of Fusarium root rot in sweetpotato, which allows for improved disease management recommendations to limit postharvest losses to this disease. }, number={8}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Scruggs, A. C. and Quesada-Ocampo, L. M.}, year={2016}, month={Aug}, pages={909–919} }
 @article{wallace_choi_thines_quesada-ocampo_2016, title={First Report of Plasmopara aff. australis on Luffa cylindrica in the United States.}, volume={100}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-06-15-0684-PDN}, DOI={10.1094/pdis-06-15-0684-pdn}, abstractNote={HomePlant DiseaseVol. 100, No. 2First Report of Plasmopara aff. australis on Luffa cylindrica in the United States PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Plasmopara aff. australis on Luffa cylindrica in the United StatesE. Wallace, Y. J. Choi, M. Thines, and L. M. Quesada-OcampoE. Wallace, Y. J. Choi, M. Thines, and L. M. Quesada-Ocampohttp://orcid.org/0000-0002-9072-7531AffiliationsAuthors and Affiliations E. Wallace , Department of Plant Pathology, North Carolina State University, Raleigh 27695 Y. J. Choi , Department of Biological Science, College of Natural Sciences, Kunsan National University, Gunsan 54150, Korea M. Thines , Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fur Naturforschung, and Johann Wolfgang Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt (Main), Germany L. M. Quesada-Ocampo , Department of Plant Pathology, North Carolina State University, Raleigh 27695. Published Online:8 Jan 2016https://doi.org/10.1094/PDIS-06-15-0684-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Luffa, or the sponge gourd, is a subtropical member of the Cucurbitaceae family. The fibrous nature of the fruit's vascular system creates a functional sponge and is mainly cultivated for this purpose. Asia and Central America lead in commercial luffa production, but the United States has recognized the demand and economic potential for luffa and efforts have been made to implement luffa as a specialty crop (Davis 2008). In August 2014, luffa leaves exhibiting irregular to angular chlorotic lesions were collected from Haywood County, North Carolina. All five luffa plants, located in a sentinel plot part of the CDM IPM pipe, were infected with 20% disease severity. The abaxial surface revealed water-soaked lesions and white sporulation consistent with downy mildew symptoms. Sporangiophores and sporangia were collected from field samples by pipetting up and down on the lesion with water, then observed and measured using a light microscope. Papillate, hyaline sporangia were primarily ovoid-spherical in shape, having dimensions of (13–) 14–15–17 (–18) × (11–) 12–13–13 (–15) (n = 54). The sporangiophore length had dimensions of (348–) 438–550–661 (–771) (n = 54). The trunk's width was (8–) 10–12–14 (–16) (n = 46), with the base slightly wider and becoming narrow just below the first branch. Branching pattern was monopodial with secondary branches and branchlets occurring at 90° angles from primary branches and secondary branches, respectively. Morphology was consistent with Plasmopara australis according to Constantinescu (2002). DNA was extracted from sporulating lesions on luffa leaves. PCR was used to amplify the nuclear gene D1-D3 region of 28S large subunit ribosomal RNA (LSU), and the mitochondrial gene cytochrome c oxidase subunit 2 (cox2) (Choi et al. 2009). Products were sequenced and submitted to GenBank (Accession Nos. KT159460 to KT159463). There is no previous sequence data available for Plasmopara australis in GenBank for BLAST analyses as occurs with many downy mildew pathogens; however, the D1-D3 nrLSU sequences were used to generate a phylogenetic tree as seen in Choi et al. 2009. Cox2 sequences were not used in phylogenetic analysis. This data, along with morphological characteristics, is sufficient to designate this pathogen P. aff. australis. Remaining tissue was preserved and submitted to the Larry F. Grand Mycological Herbarium (Catalog No. 20864). In 2006, Plasmopara australis was first reported on Luffa cylindrica in Brazil (Soares et al. 2006). In the United States, P. australis reportedly occurs on Echinocystis lobata and Sicyos angulatus, two wild cucurbit species commonly found across the country (Farr and Rossman 2015). It is unclear how L. cylindrica came to be a host for P. australis in the United States. However, this new disease is of concern for small-scale luffa growers. Certainly, more investigation may shed light on the disease cycle, epidemiology, and host-specificity of the pathogen.References:Choi, Y. J., et al. 2009. Mycol. Res. 113:1127. Crossref, Google ScholarConstantinescu, O. 2002. Sydowia 54:129. ISI, Google ScholarDavis, J. 2008. Commercial luffa sponge gourd production. Hortic. Inf. Leaflet. North Carolina State Univ. Coop. Ext., Raleigh, NC. Retrieved from http://content.ces.ncsu.edu/commercial-luffa-sponge-gourd-production, 24 March 2015. Google ScholarFarr, D. F., and Rossman, A. Y. Fungal Databases, Syst. Mycol. Microbiol. Lab., ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/, 24 March 2015. Google ScholarSoares, D. J., et al. 2006. Plant Pathol. 55:295. https://doi.org/10.1111/j.1365-3059.2006.01328.x. Crossref, ISI, Google ScholarDetailsFiguresLiterature CitedRelated Vol. 100, No. 2 February 2016SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 15 Feb 2016Published: 8 Jan 2016First Look: 15 Oct 2015Accepted: 6 Oct 2015 Pages: 537-537 Information© 2016 The American Phytopathological SocietyCited byFantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics25 February 2021 | Plants, Vol. 10, No. 3Population Analyses Reveal Two Host-Adapted Clades of Pseudoperonospora cubensis, the Causal Agent of Cucurbit Downy Mildew, on Commercial and Wild CucurbitsE. C. Wallace, K. N. D'Arcangelo, and L. M. Quesada-Ocampo7 July 2020 | Phytopathology®, Vol. 110, No. 9Diagnostic Guide for Cucurbit Downy MildewAndres Salcedo, Mary Hausbeck, Stacey Pigg, and Lina M. Quesada-Ocampo14 May 2020 | Plant Health Progress, Vol. 21, No. 3Molecular approaches for biosurveillance of the cucurbit downy mildew pathogen, Pseudoperonospora cubensis9 August 2017 | Canadian Journal of Plant Pathology, Vol. 39, No. 3}, number={2}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Wallace, E. and Choi, Y. J. and Thines, M. and Quesada-Ocampo, L. M.}, year={2016}, month={Feb}, pages={537–537} }
 @article{wolfenbarger_quesada-ocampo_gent_2016, title={Powdery Mildew Caused by Podosphaera macularis on Hop (Humulus lupulus) in North Carolina}, volume={100}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-12-15-1525-PDN}, DOI={10.1094/pdis-12-15-1525-pdn}, abstractNote={Hop (Humulus lupulus L.) production recently has expanded across the United States to include areas of the country that have not previously grown hop commercially. In June 2015, a grower in western North Carolina detected powdery mildew in a small (<0.5-ha) yard during routine scouting. Characteristic signs of powdery mildew (caused by Podosphaera macularis) were observed on cultivars ‘Cashmere’, ‘Cascade’, and ‘Chinook’. The incidence of affected leaves ranged from 0.5 to 7% among cultivars when the disease was first found, which is sufficiently severe to cause damage to cones if control measures are not implemented (Mahaffee et al. 2003). Occurrence of the disease on Cascade was of particular concern because Cascade is thought to possess some resistance to powdery mildew, although Cascade-adapted strains of P. macularis have been detected in the U.S. Pacific Northwest. Affected leaves were collected for confirmation of pathogen identity. Chasmothecia were absent. Five isolates were obtained by transferring conidia from infected leaves to healthy leaves of the powdery-mildew-susceptible cultivar Symphony. Within 7 days, powdery mildew colonies with barrel-shaped conidia and nonbranching conidiophores typical of P. macularis were visible (Ocamb et al. 1999). Two isolates from North Carolina (HPM-915 and HPM-916) and a non-Cascade-adapted isolate from Oregon (HPM-333) were each inoculated individually onto 3 leaves of Cascade (suspension of 2 × 104 conidia/ml). After 10 days of incubation at 18°C, a significantly greater number of lesions developed on leaves inoculated with isolates from North Carolina as compared with a non-Cascadeadapted isolate, indicating an adaption to this cultivar. Noninoculated controls remained Quick Links Add to favorites}, number={6}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Wolfenbarger, S. N. and Quesada-Ocampo, L. M. and Gent, D. H.}, year={2016}, month={Jun}, pages={1245–1246} }
 @article{naegele_quesada-ocampo_kurjan_saude_hausbeck_2016, title={Regional and Temporal Population Structure of Pseudoperonospora cubensis in Michigan and Ontario}, volume={106}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-02-15-0043-r}, abstractNote={ Cucurbit downy mildew (CDM), caused by the oomycete pathogen Pseudoperonospora cubensis, is a devastating disease that affects cucurbit species worldwide. This obligate, wind-dispersed pathogen does not overwinter in Michigan or other northern regions and new isolates can enter the state throughout the growing season. To evaluate the regional and temporal population structure of P. cubensis, sporangia from CDM lesions were collected from cucurbit foliage grown in Michigan and Ontario field locations in 2011. Population structure and genetic diversity were assessed in 257 isolates using nine simple sequence repeat markers. Genetic diversity was high for isolates from Michigan and Canada (0.6627 and 0.6131, respectively). Five genetic clusters were detected and changes in population structure varied by site and sampling date within a growing season. The Michigan and Canada populations were significantly differentiated, and a unique genetic cluster was detected in Michigan. }, number={4}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Naegele, R. P. and Quesada-Ocampo, L. M. and Kurjan, J. D. and Saude, C. and Hausbeck, M. K.}, year={2016}, month={Apr}, pages={372–379} }
 @article{quesada-ocampo_vargas_naegele_francis_hausbeck_2016, title={Resistance to Crown and Root Rot Caused by Phytophthora capsici in a Tomato Advanced Backcross of Solanum habrochaites and Solanum lycopersicum}, volume={100}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-08-15-0888-RE}, DOI={10.1094/pdis-08-15-0888-re}, abstractNote={ Phytophthora capsici causes devastating disease on many vegetable crops, including tomato and other solanaceous species. Solanum habrochaites accession LA407, a wild relative of cultivated tomato, has shown complete resistance to four P. capsici isolates from Michigan cucurbitaceous and solanaceous crops in a previous study. Greenhouse experiments were conducted to evaluate 62 lines of a tomato inbred backcross population between LA407 and the cultivated tomato ‘Hunt 100’ and ‘Peto 95-43’ for resistance to two highly virulent P. capsici isolates. Roots of 6-week-old seedlings were inoculated with each of two P. capsici isolates and maintained in the greenhouse. Plants were evaluated for wilting and plant death three times per week for 5 weeks. Significant differences were observed in disease response among the inbred tomato lines. Most lines evaluated were susceptible to P. capsici isolate 12889 but resistant to isolate OP97; 24 tomato lines were resistant to both isolates. Heritability of Phytophthora root rot resistance was high in this population. Polymorphic molecular markers located in genes related to resistance and defense responses were identified and added to a genetic map previously generated for the population. Resistant lines and polymorphic markers identified in this study are a valuable resource for development of tomato varieties resistant to P. capsici. }, number={4}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Vargas, A. M. and Naegele, R. P. and Francis, D. M. and Hausbeck, M. K.}, year={2016}, month={Apr}, pages={829–835} }
 @article{quesada-ocampo_al-haddad_scruggs_buell_trail_2016, title={Susceptibility of Maize to Stalk Rot Caused by Fusarium graminearum Deoxynivalenol and Zearalenone Mutants}, volume={106}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-09-15-0199-R}, DOI={10.1094/phyto-09-15-0199-r}, abstractNote={ Fusarium graminearum is a destructive pathogen of cereals that can cause stalk rot in maize. Stalk rot results in yield losses due to impaired grain filling, premature senescence, and lodging, which limits production and harvesting of ears. In addition, mycotoxins can make infected tissues unfit for silage. Our objectives were to evaluate the natural variation in stalk rot resistance among maize inbreds, to establish whether deoxynivalenol (DON)- and zearalenone (ZEA)-deficient strains are pathogenic on a panel of diverse inbreds, and to quantify the accumulation of DON in infected stalk tissue. Wild-type F. graminearum and mycotoxin mutants (DON and ZEA) were used to separately inoculate stalks of 9-week-old plants of 20 inbreds in the greenhouse. Plants were evaluated for lesion area at the inoculation point at 0, 2, 14, and 28 days postinoculation and tissues around lesions were sampled to determine the DON content. Regardless of their ability to produce DON or ZEA, all tested F. graminearum strains caused stalk rot; however, significant differences in disease levels were detected. Among the tested inbreds, Mp717 was resistant to all three F. graminearum strains while Mp317 and HP301 were only partially resistant. Accumulation of DON was significantly lower in infected stalks of the resistant and partially resistant inbreds than the susceptible inbreds. Analysis of the 20 inbreds using data from 17 simple-sequence repeats revealed population structure among the individuals; however, there was no association between genetic clustering and stalk rot resistance. These findings are an additional step toward breeding maize inbreds suitable for planting in fields infested with F. graminearum. }, number={8}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Al-Haddad, J. and Scruggs, A. C. and Buell, C. R. and Trail, F.}, year={2016}, month={Aug}, pages={920–927} }
 @article{withers_gongora-castillo_gent_thomas_ojiambo_quesada-ocampo_2016, title={Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew Pathogen}, volume={106}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-10-15-0260-FI}, DOI={10.1094/phyto-10-15-0260-fi}, abstractNote={ Advances in next-generation sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrophic obligate oomycetes that infect crops of economic importance. Unlike most downy mildew pathogens that are highly host-specific, Pseudoperonospora cubensis causes disease on a broad range of crops belonging to the family Cucurbitaceae. In this study, we identified candidate diagnostic markers for P. cubensis by comparing NGS data from a diverse panel of P. cubensis and P. humuli isolates, two very closely related oomycete species. P. cubensis isolates from diverse hosts and geographical regions in the United States were selected for sequencing to ensure that candidates were conserved in P. cubensis isolates infecting different cucurbit hosts. Genomic regions unique to and conserved in P. cubensis isolates were identified through bioinformatics. These candidate regions were then validated using PCR against a larger collection of isolates from P. cubensis, P. humuli, and other oomycetes. Overall seven diagnostic markers were found to be specific to P. cubensis. These markers could be used for pathogen diagnostics on infected tissue, or adapted for monitoring airborne inoculum with real-time PCR and spore traps. }, number={10}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Withers, S. and Gongora-Castillo, E. and Gent, D. and Thomas, A. and Ojiambo, P. S. and Quesada-Ocampo, L. M.}, year={2016}, month={Oct}, pages={1105–1116} }
 @article{rodriguez-salamanca_quesada-ocampo_naegele_hausbeck_2015, title={Characterization, Virulence, Epidemiology, and Management of Anthracnose in Celery}, volume={99}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-09-14-0994-re}, abstractNote={ Leaf curling and petiole twisting of celery (Apium graveolens) were observed in several commercial fields in five Michigan counties in 2010 through 2012, causing significant crop damage and loss. Prior to this time, the pathogen Colletotrichum acutatum species complex had not been previously associated with celery in Michigan. In this study, the pathogen’s genotype and phenotype were characterized, the influence of environmental conditions determined, and fungicides tested. Pathogen identification was based on conidial morphology and molecular identification using species-specific primers. Intersimple-sequence repeat (ISSR) banding patterns were similar between C. acutatum isolates from celery (n = 51) and blueberry (n = 1) but different from C. dematium and C. gloeosporioides. Four ISSR primers resulted in 4% polymorphism when tested on isolates from celery. Pathogenicity and virulence of C. acutatum sensu lato isolated from celery (n = 81), tomato (n = 2), and blueberry (n = 1) were evaluated in greenhouse experiments, which revealed differences in virulence among isolates but no significant differences specific to collection year, county, or field. In dew chambers and growth chambers, high temperatures (≥25°C) or long leaf wetness duration (>24 h) increased disease incidence. Twelve fungicides were tested in field studies over two growing seasons to determine their efficacy against celery anthracnose. The fungicides azoxystrobin, pyraclostrobin, mancozeb, and chlorothalonil reduced disease by 27 to 50% compared with the untreated control when disease pressure was moderate. }, number={12}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Rodriguez-Salamanca, Lina M. and Quesada-Ocampo, Lina M. and Naegele, Rachel P. and Hausbeck, Mary K.}, year={2015}, month={Dec}, pages={1832–1840} }
 @article{ojiambo_gent_quesada-ocampo_hausbeck_holmes_2015, title={Epidemiology and Population Biology of Pseudoperonospora cubensis : A Model System for Management of Downy Mildews}, volume={53}, url={http://europepmc.org/abstract/med/26002291}, DOI={10.1146/annurev-phyto-080614-120048}, abstractNote={ The resurgence of cucurbit downy mildew has dramatically influenced production of cucurbits and disease management systems at multiple scales. Long-distance dispersal is a fundamental aspect of epidemic development that influences the timing and extent of outbreaks of cucurbit downy mildew. The dispersal potential of Pseudoperonospora cubensis appears to be limited primarily by sporangia production in source fields and availability of susceptible hosts and less by sporangia survival during transport. Uncertainty remains regarding the role of locally produced inoculum in disease outbreaks, but evidence suggests multiple sources of primary inoculum could be important. Understanding pathogen diversity and population differentiation is a critical aspect of disease management and an active research area. Underpinning advances in our understanding of pathogen biology and disease management has been the research capacity and coordination of stakeholders, scientists, and extension personnel. Concepts and approaches developed in this pathosystem can guide future efforts when responding to incursions of new or reemerging downy mildew pathogens. }, number={1}, journal={Annu. Rev. Phytopathol.}, publisher={Annual Reviews}, author={Ojiambo, Peter S. and Gent, David H. and Quesada-Ocampo, Lina M. and Hausbeck, Mary K. and Holmes, Gerald J.}, year={2015}, month={Aug}, pages={223–246} }
 @misc{ojiambo_gent_quesada-ocampo_hausbeck_holmes_2015, title={Epidemiology and population biology of Pseudoperonospora cubensis: A model system for management of downy mildews}, volume={53}, journal={Annual review of phytopathology, vol 53}, author={Ojiambo, P. S. and Gent, D. H. and Quesada-Ocampo, L. M. and Hausbeck, M. K. and Holmes, G. J.}, year={2015}, pages={223–246} }
 @article{wallace_adams_quesada-ocampo_2015, title={First Report of Downy Mildew on Buffalo Gourd (Cucurbita foetidissima) Caused by Pseudoperonospora cubensis in North Carolina}, volume={99}, url={https://doi.org/10.1094/PDIS-03-15-0348-PDN}, DOI={10.1094/PDIS-03-15-0348-PDN}, abstractNote={HomePlant DiseaseVol. 99, No. 12First Report of Downy Mildew on Buffalo Gourd (Cucurbita foetidissima) Caused by Pseudoperonospora cubensis in North Carolina PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Downy Mildew on Buffalo Gourd (Cucurbita foetidissima) Caused by Pseudoperonospora cubensis in North CarolinaE. Wallace, M. Adams, and L. M. Quesada-OcampoE. WallaceSearch for more papers by this author, M. AdamsSearch for more papers by this author, and L. M. Quesada-Ocampohttp://orcid.org/0000-0002-9072-7531Search for more papers by this authorAffiliationsAuthors and Affiliations E. Wallace M. Adams L. M. Quesada-Ocampo , Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695. Published Online:1 Oct 2015https://doi.org/10.1094/PDIS-03-15-0348-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Cucurbita foetidissima (buffalo gourd) is a viny perennial crop native to the United States. This plant, characterized by long, triangular, gray-green leaves and fruits that are 5 to 10 cm in diameter and yellow at maturity, is feral and considered a weed to many. However, C. foetidissima serves several purposes in Native American cultures and its oil-rich seeds have potential economic profitability (Bemis et al. 1978; Clowney et al. 2013). C. foetidissima grows well in dry arid regions, but is widely distributed throughout the United States, growing in 22 states and Mexico (Bemis et al. 1978; USDA-NRCS PLANTS). In August through October of 2014, Pseudoperonospora cubensis was observed on C. foetidissima plants in Lenoir, Rowan, and Haywood counties in North Carolina. These plants were grown in sentinel plots as part of the CDM-IPM PIPE, the cucurbit downy mildew disease-forecasting system. The disease was characterized by irregular brown lesions with chlorotic halos and sporulation on the abaxial leaf surface. The oomycete was collected from infected leaves and observed with a microscope, revealing characteristic P. cubensis structures. An average sporangiophore trunk length of 307.6 µm and pigmented, papillated, lemon-shaped sporangia of 23.9 × 17.9 µm were observed. Sporangia collected from Lenoir County field samples were used to inoculate detached lab-grown C. foetidissima leaves. A 104/ml suspension of sporangia was applied to the abaxial surface of the leaves using a Preval sprayer. Inoculated leaves were kept in clear, acrylic boxes and placed in incubators set for a cycle of 12 h of light at 21°C then 12 h of dark at 18°C. Humidity was maintained by the addition of a damp paper towel in the box. Six days post inoculation, sporulation of the pathogen was observed on the abaxial side of the leaf. Species confirmation was also carried out molecularly. DNA was extracted from sporulating lesions and PCR was used to amplify nuclear and mitochondrial regions. PCR products were sequenced and BLAST searches showed Beta Tubulin (Btub), NADH dehydrogenase subunit 1 (Nad1), and NADH dehydrogenase subunit 5 (Nad5), had 100% identity to P. cubensis sequences in NCBI (GenBank Accession Nos. JF304706.1, KJ141003.1, and HQ636556.1, respectively). Sequences of P. cubensis isolates from C. foetidissima were added to GenBank (Accession Nos. KP970684, KP970682, and KP970683). Little is known about the impact of wild cucurbits in the yearly cucurbit downy mildew epidemic, which warrants further research. The perennial nature of C. foetidissima makes this host of particular importance, as it is believed P. cubensis may overwinter on wild cucurbits (Ojiambo et al. 2011). This is the first report of P. cubensis infecting C. foetidissima in field settings in the United States. Identifying noncommercial and wild cucurbits that host the downy mildew pathogen is an important factor to identify as we learn more about the pathogen and details of the disease cycle.References:Bemis, W., et al. 1978. Econ. Bot. 32:87. https://doi.org/10.1007/BF02906733 Crossref, ISI, Google ScholarClowney, F. G., et al. 2013. Climbers: Cucurbita foetidissima. University of Michigan. Retrieved from http://climbers.lsa.umich.edu/?p=258, 11 August 2014. Google ScholarUSDA-NRCS. PLANTS Database. Natural Resources Conservation Service, USDA. Retrieved from http://plants.usda.gov, 22 August 2014. Google ScholarOjiambo P.S., et al. 2011. Plant Health Progress https://doi.org/10.1094/PHP-2011-0411-01-RV. Google ScholarDetailsFiguresLiterature CitedRelated Vol. 99, No. 12 December 2015SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 16 Dec 2015Published: 1 Oct 2015First Look: 15 Jun 2015Accepted: 7 Jun 2015 Pages: 1861-1861 Information© 2015 The American Phytopathological SocietyCited byCarboxylic Acid Amide but Not Quinone Outside Inhibitor Fungicide Resistance Mutations Show Clade-Specific Occurrence in Pseudoperonospora cubensis Causing Downy Mildew in Commercial and Wild CucurbitsK. N. D'Arcangelo, E. C. Wallace, T. D. Miles, and L. M. Quesada-Ocampo12 January 2023 | Phytopathology®, Vol. 113, No. 1Field Occurrence and Overwintering of Oospores of Pseudoperonospora cubensis in the Southeastern United StatesIsaack Kikway, Anthony P. Keinath, and Peter S. Ojiambo8 August 2022 | Phytopathology®, Vol. 112, No. 9Pseudoperonospora cubensis (cucumber downy mildew)CABI Compendium, Vol. CABI CompendiumDiseases of Cucumbers, Melons, Pumpkins, Squash, and Watermelons30 August 2022Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics25 February 2021 | Plants, Vol. 10, No. 3Clade-Specific Biosurveillance of Pseudoperonospora cubensis Using Spore Traps for Precision Disease Management of Cucurbit Downy MildewA. Rahman, J. R. Standish, K. N. D’Arcangelo, and L. M. Quesada-Ocampo16 January 2021 | Phytopathology®, Vol. 111, No. 2Assessment of fungicide product applications and program approaches for control of downy mildew on pickling cucumber in North CarolinaCrop Protection, Vol. 140Simultaneous detection of downy mildew and powdery mildew pathogens on Cucumis sativus and other cucurbits using duplex-qPCR and HRM analysis3 August 2020 | AMB Express, Vol. 10, No. 1Population Analyses Reveal Two Host-Adapted Clades of Pseudoperonospora cubensis, the Causal Agent of Cucurbit Downy Mildew, on Commercial and Wild CucurbitsE. C. Wallace, K. N. D’Arcangelo, and L. M. Quesada-Ocampo7 July 2020 | Phytopathology®, Vol. 110, No. 9QTL Analysis for Downy Mildew Resistance in Cucumber Inbred Line PI 197088Lixia Li, Huiqiang He, Zhirong Zou, and Yuhong Li27 April 2018 | Plant Disease, Vol. 102, No. 7Molecular approaches for biosurveillance of the cucurbit downy mildew pathogen, Pseudoperonospora cubensis9 August 2017 | Canadian Journal of Plant Pathology, Vol. 39, No. 3Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations2 May 2017 | PeerJ, Vol. 5Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew PathogenS. Withers, E. Gongora-Castillo, D. Gent, A. Thomas, P. S. Ojiambo, and L. M. Quesada-Ocampo17 June 2016 | Phytopathology®, Vol. 106, No. 10}, number={12}, journal={Plant Disease}, publisher={Scientific Societies}, author={Wallace, E. and Adams, M. and Quesada-Ocampo, L. M.}, year={2015}, month={Dec}, pages={1861–1861} }
 @article{kousik_parada_quesada-ocampo_2015, title={First Report of Phytophthora Fruit Rot on Bitter Gourd (Mormodica charantia) and Sponge Gourd (Luffa cylindrica) Caused by Phytophthora capsici}, DOI={10.1094/php-br-15-0005}, abstractNote={ Luffa sponge (smooth gourd) and bitter gourds (bitter melon) are specialty vegetables grown in the U.S. on a small scale for select markets. Luffa gourds are also grown for sponges. In Sept. 2014, heavy rainfall resulted in rot of >50% of bitter gourd and >25% on sponge gourd in a field in Charleston, SC. The microbe causing the fruit rot was identified using microscopy and molecular tools. Prior to this study it was not known if this microbe could cause fruit rot of bitter gourd. This knowledge will be useful to suggest management strategies.  Accepted for publication 17 March 2015. Published 6 May 2015. }, journal={PHP}, publisher={Scientific Societies}, author={Kousik, Chandrasekar S. and Parada, Camilo and Quesada-Ocampo, Lina}, year={2015} }
 @article{quesada-ocampo_withers_butler_birdsell_schultheis_2015, title={First Report of Plectosporium Blight on Pumpkin and Squash Caused by Plectosporium tabacinum in North Carolina}, volume={99}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-07-14-0770-pdn}, abstractNote={HomePlant DiseaseVol. 99, No. 5First Report of Plectosporium Blight on Pumpkin and Squash Caused by Plectosporium tabacinum in North Carolina PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Plectosporium Blight on Pumpkin and Squash Caused by Plectosporium tabacinum in North CarolinaL. M. Quesada-Ocampo, S. Withers, S. Butler, T. Birdsell, and J. SchultheisL. M. Quesada-OcampoSearch for more papers by this author, S. WithersSearch for more papers by this author, S. ButlerSearch for more papers by this author, T. BirdsellSearch for more papers by this author, and J. SchultheisSearch for more papers by this authorAffiliationsAuthors and Affiliations L. M. Quesada-Ocampo S. Withers S. Butler , Department of Plant Pathology, North Carolina State University, Raleigh 27695 T. Birdsell , Cooperative Extension, North Carolina State University, Raleigh 27695 J. Schultheis , Department of Horticulture, North Carolina State University, Raleigh 27695. Published Online:29 May 2015https://doi.org/10.1094/PDIS-07-14-0770-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Cucurbits are among the most important vegetable crops in North Carolina. Plectosporium blight, caused by Plectosporium tabacinum, can significantly reduce marketable fruit in squash and pumpkin (1). Since 1988, when Plectosporium blight was first reported in the United States in Tennessee, the disease has been confirmed in New York, Alabama, Louisiana, Virginia, and Illinois (4). In July of 2013, approximately15% of zucchini squash (Cucurbita pepo ‘Zephyr’ and ‘Senator’) grown in an organic commercial field in Davidson County, NC, showed spindle-shaped, corky, sunken, tan lesions on the stems and petioles; and circular, corky, raised, tan lesions on the leaves and fruit. In September of 2013, approximately 10 to 20% of the pumpkin plants (C. pepo ‘Field Trip’) at research station fields in Ashe and Haywood Counties, NC, also showed stem, leaf, and fruit lesions characteristic of Plectosporium blight (4). After surface-sterilization with 70% ethanol, four to five lesions were excised from petioles and fruit of each cultivar, placed on potato dextrose agar, and incubated under constant fluorescent light at room temperature (21°C). Tan to light pink colonies with white aerial mycelium grew on the plates after a week, and after single-sporing, one representative isolate from each of three cultivars, Zephyr, Senator, and Field Trip, was retained for analysis. One- and two-celled, hyaline, elongate, ellipsoid, slightly curved conidia (n = 10), each with a narrow base that measured 7.4 to 10.2 × 2.1 to 3 μm were observed for the three isolates at 100× magnification. Branched, hyaline conidiophores (n = 5) with elongate, slightly sinuous, apical phialides and conidia in mucilaginous heads at the tip of each conidiophore identified the isolates as P. tabacinum (synonyms Microdochium tabacinum, Fusarium tabacinum, and Plectosphaerella cucumerina) (2). To confirm the identity of the isolates, the internal transcribed spacer (ITS) region of ribosomal DNA was amplified and sequenced with the ITS4 and ITS5 primers (3). The sequence was compared with sequences in GenBank using a BLAST alignment, which revealed that the isolates had 98% identity with ITS sequences of P. cucumerina (AB266250.1), the teleomorph of P. tabacinum. The ITS sequences of the three isolates were deposited in GenBank under accession numbers KJ130026, KJ130027, and KJ130028. No official report has been published of P. tabacinum on C. pepo in NC; however, Plectosporium blight can be misidentified as mechanical injury, e.g., from sand blasting, and it is likely that the pathogen has previously been encountered but not yet reported officially in NC. While it is uncommon for Plectosporium blight to result in devastating yield losses, the disease can cause significant reduction in marketable fruit, which may warrant applications of effective fungicides in fields where the pathogen has been found.References:(1) Mullen, J. M., and Sikora, E. J. 2003. Plant Dis. 87:749. https://doi.org/10.1094/PDIS.2003.87.6.749A Link, ISI, Google Scholar(2) Palm, M. E., et al. 1995. Mycologia 87:397. https://doi.org/10.2307/3760837 Crossref, ISI, Google Scholar(3) White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, CA. Crossref, Google Scholar(4) Zitter, T. A. 1996. Page 28 in: Compendium of Cucurbit Diseases. T. A. Zitter, D. L. Hopkins, and C. E. Thomas, eds. The American Phytopathological Society, St. Paul, MN. Google ScholarDetailsFiguresLiterature CitedRelated Vol. 99, No. 5 May 2015SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 29 May 2015Published: 29 May 2015First Look: 11 Dec 2014Accepted: 3 Dec 2014 Page: 724 Information© 2015 The American Phytopathological SocietyCited byPlectosphaerella cucumerinaCABI Compendium, Vol. CABI CompendiumDiseases of Chrysanthemum7 January 2018Diseases of Chrysanthemum24 May 2017}, number={5}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Withers, S. and Butler, S. and Birdsell, T. and Schultheis, J.}, year={2015}, month={May}, pages={724–725} }
 @article{holmes_ojiambo_hausbeck_quesada-ocampo_keinath_2015, title={Resurgence of Cucurbit Downy Mildew in the United States: A Watershed Event for Research and Extension}, volume={99}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-09-14-0990-fe}, abstractNote={ In 2004, an outbreak of cucurbit downy mildew (CDM) caused by the oomycete Pseudoperonospora cubensis (Berk. & M. A. Curtis) Rostovzev resulted in an epidemic that stunned the cucumber (Cucumis sativus L.) industry in the eastern United States. The disease affects all major cucurbit crops, including cucumber, muskmelon, squashes, and watermelon. Although the 2004 epidemic began in North Carolina, the cucumber crop from Florida to the northern growing regions in the United States was devastated, resulting in complete crop loss in several areas. Many cucumber fields were abandoned prior to harvest. The rapid spread of the disease coupled with the failure of fungicide control programs surprised growers, crop consultants, and extension specialists. The epidemic raised several fundamental questions about the potential causes for the resurgence of the disease. Some of these questions revolved around whether the epidemic would recur in subsequent years and the possible roles that changes in the host, pathogen, and environment may have played in the epidemic. }, number={4}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Holmes, Gerald and Ojiambo, Peter and Hausbeck, Mary and Quesada-Ocampo, Lina and Keinath, Anthony}, year={2015}, month={Apr}, pages={428–441} }
 @article{holmes_ojiambo_hausbeck_quesada-ocampo_keinath_2015, title={Resurgence of Cucurbit Downy Mildew in the United States: A Watershed Event for Research and Extension}, volume={4015}, DOI={10.1094/pdis-09-14-0990-fe.testissue}, number={1}, journal={Plant Disease}, publisher={Scientific Societies}, author={Holmes, Gerald J. and Ojiambo, Peter S. and Hausbeck, Mary K. and Quesada-Ocampo, Lina and Keinath, Anthony P.}, year={2015}, month={Jan}, pages={1–14} }
 @article{cohen_langenberg_wehner_ojiambo_hausbeck_quesada-ocampo_lebeda_sierotzki_gisi_2015, title={Resurgence of Pseudoperonospora cubensis: The Causal Agent of Cucurbit Downy Mildew}, volume={105}, ISSN={["1943-7684"]}, url={http://europepmc.org/abstract/med/25844827}, DOI={10.1094/phyto-11-14-0334-fi}, abstractNote={ The downy mildew pathogen, Pseudoperonospora cubensis, which infects plant species in the family Cucurbitaceae, has undergone major changes during the last decade. Disease severity and epidemics are far more destructive than previously reported, and new genotypes, races, pathotypes, and mating types of the pathogen have been discovered in populations from around the globe as a result of the resurgence of the disease. Consequently, disease control through host plant resistance and fungicide applications has become more complex. This resurgence of P. cubensis offers challenges to scientists in many research areas including pathogen biology, epidemiology and dispersal, population structure and population genetics, host preference, host−pathogen interactions and gene expression, genetic host plant resistance, inheritance of host and fungicide resistance, and chemical disease control. This review serves to summarize the current status of this major pathogen and to guide future management and research efforts within this pathosystem. }, number={7}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Cohen, Yigal and Langenberg, Kyle M. and Wehner, Todd C. and Ojiambo, Peter S. and Hausbeck, Mary and Quesada-Ocampo, Lina M. and Lebeda, Ales and Sierotzki, Helge and Gisi, Ulrich}, year={2015}, month={Jul}, pages={998–1012} }
 @article{scruggs_butler_quesada-ocampo_2014, title={First Report of Cladosporium Leaf Spot of Spinach Caused by Cladosporium variabile in North Carolina}, volume={98}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-05-14-0474-pdn}, abstractNote={ Cladosporium leaf spot of spinach, caused by Cladosporium variabile, can result in significant economic losses in the United States (2). In March 2014, symptoms consistent with Cladosporium leaf spot (4) appeared on the spinach cultivar Tyee in a greenhouse located in Rowan County, NC. Of 1,080 spinach plants, 90 to 100% were infected. Symptoms consisted of small (1 to 3 mm in diameter), circular, tan lesions each outlined with a dark margin on the adaxial surface of the leaf. On severely infected foliage, lesions coalesced to produce relatively large necrotic regions. Profuse fungal sporulation was observed on the lesion surface with a dissecting microscope at 40× magnification. Using a dissecting microscope, conidia were collected with a sterile needle and transferred to petri plates containing potato dextrose agar. Plates were then incubated at 23 ± 2°C under continuous fluorescent light, and fungal growth was apparent after 24 h. Isolations from leaves of six infected plants produced slow-growing, dark green to brown fungal colonies that reached only 31 mm in diameter after 14 days, which is characteristic of C. variabile (4). Colonies contained dense masses of dematiaceous, septate, unbranched conidiophores with conidial chains, each containing up to five conidia. Conidia were ovate to elongate, with some being septate. The length of individual conidia ranged from 10 to 19 μm. Conidial septa were distinctly dark when observed at 100× magnification, which is a defining feature of C. variabile vs. the conidia of C. macrocarpum (4). The surface of the conidia appeared verrucose at 100× magnification, and conidia were each distinctly darkened toward the base. A single isolate obtained through single-spore transfer was used for DNA extraction, and the histone 3 (H3) gene sequence was amplified using the primers CYLH3F and CYLH3R (1). Sequence analysis of the amplified product using BLAST analysis indicated that the H3 sequences had 100% identity to that of a C. variabile isolate (GenBank Accession No. EF679710.1), and 99% identity to a C. macrocarpum isolate (EF679687.1). The H3 sequence from a representative isolate was deposited in GenBank (KJ769146). To our knowledge, this is the first report of Cladosporium leaf spot on spinach in North Carolina based on morphological evaluation and H3 sequencing results. C. variabile is a seedborne pathogen, so it is possible inoculum was introduced into the greenhouses in North Carolina on infected seed (3). Seeds can be treated with hot water or chlorine to reduce the risk of disease outbreaks caused by infected seed (2). Furthermore, Cladosporium leaf spot may be controlled with the use of fungicides (3).  References: (1) P. Crous et al. Stud. Mycol. 50:415, 2004. (2) L. J. du Toit and P. Hernandez-Perez. Plant Dis. 89:1305, 2005. (3) L. J. du Toit et al. Fung. Nemat. Tests 59:V115, 2004. (4) Schubert et al. Stud. Mycol. 58:105, 2007. }, number={12}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Scruggs, A. C. and Butler, S. C. and Quesada-Ocampo, L. M.}, year={2014}, month={Dec} }
 @article{quesada-ocampo_butler_withers_ivors_2014, title={First Report of Fusarium Rot of Garlic Bulbs Caused by Fusarium proliferatum in North Carolina}, volume={98}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-01-14-0040-pdn}, abstractNote={ In August of 2013, garlic bulbs (Allium sativum) of the variety Chesnok Red grown and stored under dry conditions by a commercial producer in Buncombe County showed water-soaked, tan to salmon-pink lesions. Lesions on cloves became soft over time, slightly sunken, and had mycelium near the center of the bulb, which is characteristic of Fusarium rots on garlic (1,2). Approximately 10 to 20% of the bulbs inspected in the drying storage room were affected. Surface-sterilized tissue was excised from the margin of lesions on eight bulbs, plated onto acid potato dextrose agar (APDA), and incubated in the dark at room temperature (21°C). White to light pink colonies with abundant aerial mycelium and a purple pigment were obtained from all samples after 2 to 3 days of incubation. Inspection of colony morphology and reproductive structures under a microscope revealed that isolate characteristics were consistent with Fusarium proliferatum (Matsushima) Nirenberg. Microscopic morphological characteristics of the isolate included hyaline, septate hyphae; slender, slightly curved macroconidia with three to five septae produced in sporodochia; curved apical cell; and club-shaped, aseptate microconidia (measuring 3.3 to 8.3 × 1.1 to 1.3 μm) produced in chains by mono and polyphyalides. To further define the identity of the isolate, the beta-tubulin (Btub), elongation factor 1a (EF1a), and internal transcribed spacer (ITS) regions were amplified and sequenced (3). The resulting sequences were compared against the GenBank nucleotide database by using a BLAST alignment, which revealed that the isolate had 100% identity with F. proliferatum for the Btub, EF1a, and ITS regions (GenBank Accession Nos. AF291055.1, JX118976.1, and HF930594.1, respectively). Sequences for the isolate were deposited in GenBank under accessions KJ128963, KJ128964, and KJ128965. While there have been other reports of F. proliferatum causing bulb rot of garlic in the United States (1), to our knowledge, this is the first report in North Carolina. The finding is significant since F. proliferatum can produce a broad range of mycotoxins, including fumonisins, when infecting its host, which is a concern for food safety in Allium crops.  References: (1) F. M. Dugan et al. Plant Pathol. 52:426, 2003. (2) L. J. du Toit and F. M. Dugan. Page 15 in: Compendium of Onion and Garlic Diseases and Pests. H. F. Schwartz and S. K. Mohan, eds. The American Phytopathological Society, St. Paul, MN, 2008. (3) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, CA, 1990. }, number={7}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Butler, S. and Withers, S. and Ivors, K.}, year={2014}, month={Jul}, pages={1009–1010} }
 @article{wallace_adams_ivors_ojiambo_quesada-ocampo_2014, title={First Report of Pseudoperonospora cubensis Causing Downy Mildew on Momordica balsamina and M. charantia in North Carolina}, volume={98}, ISSN={["1943-7692"]}, url={http://europepmc.org/abstract/med/30699625}, DOI={10.1094/pdis-03-14-0305-pdn}, abstractNote={ Momordica balsamina (balsam apple) and M. charantia L. (bitter melon/bitter gourd/balsam pear) commonly grow in the wild in Africa and Asia; bitter melon is also cultivated for food and medicinal purposes in Asia (1). In the United States, these cucurbits grow as weeds or ornamentals. Both species are found in southern states and bitter melon is also found in Pennsylvania and Connecticut (3). Cucurbit downy mildew (CDM), caused by the oomycete Pseudoperonospora cubensis, was observed on bitter melon and balsam apple between August and October of 2013 in six North Carolina sentinel plots belonging to the CDM ipmPIPE program (2). Plots were located at research stations in Johnston, Sampson, Lenoir, Henderson, Rowan, and Haywood counties, and contained six different commercial cucurbit species including cucumbers, melons, and squashes in addition to the Momordica spp. Leaves with symptoms typical of CDM were collected from the Momordica spp. and symptoms varied from irregular chlorotic lesions to circular lesions with chlorotic halos on the adaxial leaf surface. Sporulation on the abaxial side of the leaves was observed and a compound microscope revealed sporangiophores (180 to 200 μm height) bearing lemon-shaped, dark sporangia (20 to 35 × 10 to 20 μm diameter) with papilla on one end. Genomic DNA was extracted from lesions and regions of the NADH dehydrogynase subunit 1 (Nad1), NADH dehydrogynase subunit 5 (Nad5), and internal transcribed spacer (ITS) ribosomal RNA genes were amplified and sequenced (4). BLAST analysis revealed 100% identity to P. cubensis Nad1 (HQ636552.1, HQ636551.1), Nad5 (HQ636556.1), and ITS (HQ636491.1) sequences in GenBank. Sequences from a downy mildew isolate from each Momordica spp. were deposited in GenBank as accession nos. KJ496339 through 44. To further confirm host susceptibility, vein junctions on the abaxial leaf surface of five detached leaves of lab-grown balsam apple and bitter melon were either inoculated with a sporangia suspension (10 μl, 104 sporangia/ml) of a P. cubensis isolate from Cucumis sativus (‘Vlaspik' cucumber), or with water as a control. Inoculated leaves were placed in humidity chambers to promote infection and incubated using a 12-h light (21°C) and dark (18°C) cycle. Seven days post inoculation, CDM symptoms and sporulation were observed on inoculated balsam apple and bitter melon leaves. P. cubensis has been reported as a pathogen of both hosts in Iowa (5). To our knowledge, this is the first report of P. cubensis infecting these Momordica spp. in NC in the field. Identifying these Momordica spp. as hosts for P. cubensis is important since these cucurbits may serve as a source of CDM inoculum and potentially an overwintering mechanism for P. cubensis. Further research is needed to establish the role of non-commercial cucurbits in the yearly CDM epidemic, which will aid the efforts of the CDM ipmPIPE to predict disease outbreaks.  References: (1) L. K. Bharathi and K. J. John. Momordica Genus in Asia-An Overview. Springer, New Delhi, India, 2013. (2) P. S. Ojiambo et al. Plant Health Prog. doi:10.1094/PHP-2011-0411-01-RV, 2011. (3) PLANTS Database. Natural Resources Conservation Service, USDA. Retrieved from http://plants.usda.gov/ , 7 February 2014. (4) L. M. Quesada-Ocampo et al. Plant Dis. 96:1459, 2012. (5) USDA. Index of Plant Disease in the United States. Agricultural Handbook 165, 1960. }, number={9}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Wallace, E. and Adams, M. and Ivors, K. and Ojiambo, P. S. and Quesada-Ocampo, L. M.}, year={2014}, month={Sep}, pages={1279–1279} }
 @article{naegele_boyle_quesada-ocampo_hausbeck_2014, title={Genetic Diversity, Population Structure, and Resistance to Phytophthora capsici of a Worldwide Collection of Eggplant Germplasm}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0095930}, abstractNote={Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.}, number={5}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Naegele, Rachel P. and Boyle, Samantha and Quesada-Ocampo, Lina M. and Hausbeck, Mary K.}, editor={Vinatzer, Boris AlexanderEditor}, year={2014}, month={May} }
 @article{kawahara_bastide_hamilton_kanamori_mccombie_ouyang_schwartz_tanaka_wu_zhou_et al._2013, title={Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data}, volume={6}, DOI={10.1186/1939-8433-6-4}, abstractNote={Abstract
          
            Background
            Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).
          
          
            Results
            The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.
          
          
            Conclusions
            A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
          }, number={1}, journal={Rice}, publisher={Springer Science \mathplus Business Media}, author={Kawahara, Yoshihiro and Bastide, Melissa and Hamilton, John P and Kanamori, Hiroyuki and McCombie, W Richard and Ouyang, Shu and Schwartz, David C and Tanaka, Tsuyoshi and Wu, Jianzhong and Zhou, Shiguo and et al.}, year={2013}, pages={4} }
 @article{granke_quesada-ocampo_hausbeck, title={Phytophthora capsici in the eastern USA.}, DOI={10.1079/9781780640938.0096}, abstractNote={Phytophthora capsici was first documented in the eastern USA in Florida in 1931 and was subsequently reported in New York in 1935, New Jersey around 1970, South Carolina in 1994, Michigan in 1997 and Illinois in 1999. The host range, epidemiology in the eastern USA, isolating from plant tissue, water and soil, variation in morphology and virulence within P. capsici, genetic diversity and population dynamics, disease management, and future prospects on P. capsici are discussed.}, journal={Phytophthora: a global perspective}, publisher={CABI Publishing}, author={Granke, L. and Quesada-Ocampo, L. and Hausbeck, M.}, pages={96–103} }
 @article{granke_quesada-ocampo_lamour_hausbeck_2012, title={Advances in Research on Phytophthora capsici on Vegetable Crops in The United States}, volume={96}, DOI={10.1094/pdis-02-12-0211-fe}, abstractNote={ Since L. H. Leonian's first description of Phytophthora capsici as a pathogen of chile pepper in 1922, we have made many advances in our understanding of this pathogen's biology, host range, dissemination, and management. P. capsici causes foliar blighting, damping-off, wilting, and root, stem, and fruit rot of susceptible hosts, and economic losses are experienced annually in vegetable crops including cucurbits and peppers. Symptoms of P. capsici infection may manifest as stunting, girdling, or cankers for some cultivars or crops that are less susceptible. P. capsici continues to be a constraint on production, and implementation of an aggressive integrated management scheme can still result in insufficient control when weather is favorable for disease. Management of diseases caused by P. capsici is currently limited by the long-term survival of the pathogen as oospores in the soil, a wide host range, long-distance movement of the pathogen in surface water used for irrigation, the presence of fungicide-resistant pathogen populations, and a lack of commercially acceptable resistant host varieties. P. capsici can infect a wide range of hosts under laboratory and greenhouse conditions including cultivated crops, ornamentals, and native plants belonging to diverse plant families. As our understanding of P. capsici continues to grow, future research should focus on developing novel and effective solutions to manage this pathogen and prevent economic losses due to the diseases it causes. }, number={11}, journal={Plant Disease}, publisher={Scientific Societies}, author={Granke, Leah L. and Quesada-Ocampo, Lina and Lamour, Kurt and Hausbeck, Mary K.}, year={2012}, month={Nov}, pages={1588–1600} }
 @article{quesada-ocampo_landers_lebeis_fulbright_hausbeck_2012, title={Genetic Structure of Clavibacter michiganensis subsp. michiganensis Populations in Michigan Commercial Tomato Fields}, volume={96}, DOI={10.1094/pdis-05-11-0402}, abstractNote={ Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial canker of tomato, is distinguished into four fingerprint types (A, B, C, and D) using BOX-polymerase chain reaction (PCR). To characterize the variation within the C. michiganensis subsp. michiganensis population in Michigan, 718 strains of C. michiganensis subsp. michiganensis were isolated from infected foliage and fruit collected from 14 and 9 Michigan commercial tomato fields in 1997 and 1998, respectively. The frequency of PCR types detected with BOX-PCR in all strains, and Bayesian cluster analysis, pairwise differentiation index comparisons, and genetic diversity estimates of 96 strains genotyped for six virulence-related genes revealed that C. michiganensis subsp. michiganensis populations in Michigan tomato fields are geographically structured. A multilocus haplotype cladogram was also consistent with geographic stratification in C. michiganensis subsp. Michiganensis populations. Some regions had strains predominantly of only one PCR type or belonging mostly to one genetic cluster, while other regions presented more diversity of occurrence of PCR types and genetic clusters. Results derived from this study provide information about the genetic structure of C. michiganensis subsp. michiganensis populations in Michigan and genetic diversity of C. michiganensis subsp. michiganensis inocula, which is key in developing disease management strategies. }, number={6}, journal={Plant Disease}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Landers, N. A. and Lebeis, A. C. and Fulbright, D. W. and Hausbeck, M. K.}, year={2012}, month={Jun}, pages={788–796} }
 @article{quesada-ocampo_granke_olsen_gutting_runge_thines_lebeda_hausbeck_2012, title={The Genetic Structure of Pseudoperonospora cubensis Populations}, volume={96}, DOI={10.1094/pdis-11-11-0943-re}, abstractNote={ Pseudoperonospora cubensis is a destructive foliar pathogen of economically important cucurbitaceous crops in the United States and worldwide. In this study, we investigated the genetic structure of 465 P. cubensis isolates from three continents, 13 countries, 19 states of the United States, and five host species using five nuclear and two mitochondrial loci. Bayesian clustering resolved six genetic clusters and suggested some population structure by geographic origin and host, because some clusters occurred more or less frequently in particular categories. All of the genetic clusters were present in the sampling from North America and Europe. Differences in cluster occurrence were observed by country and state. Isolates from cucumber had different cluster composition and lower genetic diversity than isolates from other cucurbits. Because genetic structuring was detected, isolates that represent the genetic variation in P. cubensis should be used when developing diagnostic tools, fungicides, and resistant host varieties. Although this study provides an initial map of global population structure of P. cubensis, future genotyping of isolates could reveal population structure within specific geographic regions, across a wider range of hosts, or during different time points during the growing season. }, number={10}, journal={Plant Disease}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Granke, L. L. and Olsen, J. and Gutting, H. C. and Runge, F. and Thines, M. and Lebeda, A. and Hausbeck, M. K.}, year={2012}, month={Oct}, pages={1459–1470} }
 @article{granke_quesada-ocampo_hausbeck_2012, title={Differences in virulence of Phytophthora capsici isolates from a worldwide collection on host fruits}, volume={132}, ISSN={0929-1873 1573-8469}, url={http://dx.doi.org/10.1007/S10658-011-9873-4}, DOI={10.1007/S10658-011-9873-4}, number={2}, journal={European Journal of Plant Pathology}, publisher={Springer Science and Business Media LLC}, author={Granke, Leah L. and Quesada-Ocampo, Lina M. and Hausbeck, Mary K.}, year={2012}, month={Feb}, pages={281–296} }
 @article{quesada-ocampo_granke_mercier_olsen_hausbeck_2011, title={Investigating the Genetic Structure of Phytophthora capsici Populations}, volume={101}, DOI={10.1094/phyto-11-10-0325}, abstractNote={Phytophthora capsici Leonian is a destructive soilborne pathogen that infects economically important solanaceous, cucurbitaceous, fabaceous, and other crops in the United States and worldwide. The objective of this study was to investigate the genetic structure of 255 P. capsici isolates assigned to predefined host, geographical, mefenoxam-sensitivity, and mating-type categories. Isolates from six continents, 21 countries, 19 U.S. states, and 26 host species were genotyped for four mitochondrial and six nuclear loci. Bayesian clustering revealed some population structure by host, geographic origin, and mefenoxam sensitivity, with some clusters occurring more or less frequently in particular categories. Bayesian clustering, split networks, and statistical parsimony genealogies also detected the presence of non-P. capsici individuals in our sample corresponding to P. tropicalis (n = 9) and isolates of a distinct cluster closely related to P. capsici and P. tropicalis (n = 10). Our findings of genetic structuring in P. capsici populations highlight the importance of including isolates from all detected clusters that represent the genetic variation in P. capsici for development of diagnostic tools, fungicides, and host resistance. The population structure detected will also impact the design and interpretation of association studies in P. capsici. This study provides an initial map of global population structure of P. capsici but continued genotyping of isolates will be necessary to expand our knowledge of genetic variation in this important plant pathogen.}, number={9}, journal={Phytopathology}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Granke, L. L. and Mercier, M. R. and Olsen, J. and Hausbeck, M. K.}, year={2011}, month={Sep}, pages={1061–1073} }
 @article{quesada-ocampo_granke_hausbeck_2011, title={Temporal Genetic Structure of Phytophthora capsici Populations from a Creek Used for Irrigation in Michigan}, volume={95}, DOI={10.1094/pdis-03-11-0191}, abstractNote={Irrigation water may harbor Phytophthora capsici, and irrigating susceptible vegetable crops with infested water can initiate epidemics. In this study, we evaluated the genetic structure of 106 P. capsici isolates collected from a creek used for irrigation (2002, 2003, and 2006) and from a field adjacent to the creek (2001) using six polymorphic nuclear loci. Bayesian clustering analysis detected four clusters in the sample, and some clusters occurred more or less frequently in certain years. In 2006, isolates belonging to cluster four predominated in the sampling. Mean pairwise FSTvalues (0.008 to 0.065) indicated low differentiation between categories, but the most differentiation was observed when 2006 was compared to 2001 and 2002. Differences in isolate phenotypic traits were observed year-to-year. Isolates insensitive to mefenoxam were more common in 2006 and 2003 than in 2002 and 2001. The mating type ratio was approximately 1:1 in 2002 and 2003, but was skewed toward A1 in 2001 and toward A2 in 2006. Since irrigation water can remain infested or become reinfested annually with P. capsici for years after the adjacent fields are transitioned to nonsusceptible crops, growers are advised to avoid potentially infested irrigation water even after rotating to nonhost crops for several years.}, number={11}, journal={Plant Disease}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Granke, L. L. and Hausbeck, M. K.}, year={2011}, month={Nov}, pages={1358–1369} }
 @article{granke_quesada-ocampo_hausbeck_2011, title={Variation in Phenotypic Characteristics of Phytophthora capsici Isolates from a Worldwide Collection}, volume={95}, DOI={10.1094/pdis-03-11-0190}, abstractNote={ To determine variation within Phytophthora capsici, 124 P. capsici isolates from 12 countries were characterized for sporangial length and width, pedicle length, oospore diameter, sporangia and chlamydospore production, and growth at 32, 35, and 38°C. Sporangia were 23 to 35 μm wide and 38 to 60 μm long; differences in width and length were noted when isolates were grouped by genetic cluster and continent of origin. Length:breadth ratio (1.34 to 2.07) and pedicle length (20 to 260 μm long) varied widely among isolates; differences were apparent by continent and host family of origin. Oospore diameters varied among isolates (22 to 37 μm), but no differences were noted by isolate genetic cluster, host family of origin, continent of origin, mating type, or sensitivity to mefenoxam. Differences in sporangia production were observed among isolates grouped by continent, and isolates from nonvegetable hosts produced fewer sporangia than isolates from vegetable hosts. When cultures were incubated in a liquid medium, 35 P. capsici isolates formed chlamydospores. Most (122 of 124) of the isolates were able to grow at 35°C, but all of the isolates grew poorly at 38°C. The results of this study indicate substantial variation in morphological and physiological characteristics among P. capsici isolates. }, number={9}, journal={Plant Disease}, publisher={Scientific Societies}, author={Granke, L. L. and Quesada-Ocampo, L. M. and Hausbeck, M. K.}, year={2011}, month={Sep}, pages={1080–1088} }
 @article{quesada-ocampo_hausbeck_2010, title={Resistance in Tomato and Wild Relatives to Crown and Root Rot Caused by Phytophthora capsici}, volume={100}, DOI={10.1094/phyto-100-6-0619}, abstractNote={ Phytophthora capsici causes root, crown, and fruit rot of tomato, a major vegetable crop grown worldwide. The objective of this study was to screen tomato cultivars and wild relatives of tomato for resistance to P. capsici. Four P. capsici isolates were individually used to inoculate 6-week-old seedlings (1 g of P. capsici-infested millet seed per 10 g of soilless medium) of 42 tomato cultivars and wild relatives of tomato in a greenhouse. Plants were evaluated daily for wilting and death. All P. capsici isolates tested caused disease in seedlings but some isolates were more pathogenic than others. A wild relative of cultivated tomato, Solanum habrochaites accession LA407, was resistant to all P. capsici isolates tested. Moderate resistance to all isolates was identified in the host genotypes Ha7998, Fla7600, Jolly Elf, and Talladega. P. capsici was frequently recovered from root and crown tissue of symptomatic inoculated seedlings but not from leaf tissue or asymptomatic or control plants. The phenotype of the recovered isolate matched the phenotype of the inoculum. Pathogen presence was confirmed in resistant and moderately resistant tomato genotypes by species-specific polymerase chain reaction of DNA from infected crown and root tissue. Amplified fragment length polymorphisms of tomato genotypes showed a lack of correlation between genetic clusters and susceptibility to P. capsici, indicating that resistance is distributed in several tomato lineages. The results of this study create a baseline for future development of tomato cultivars resistant to P. capsici. }, number={6}, journal={Phytopathology}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Hausbeck, M. K.}, year={2010}, month={Jun}, pages={619–627} }
 @article{savory_granke_quesada-ocampo_varbanova_hausbeck_brad_2010, title={The cucurbit downy mildew pathogen Pseudoperonospora cubensis}, volume={12}, DOI={10.1111/j.1364-3703.2010.00670.x}, abstractNote={SUMMARY Pseudoperonospora cubensis[(Berkeley & M. A. Curtis) Rostovzev], the causal agent of cucurbit downy mildew, is responsible for devastating losses worldwide of cucumber, cantaloupe, pumpkin, watermelon and squash. Although downy mildew has been a major issue in Europe since the mid‐1980s, in the USA, downy mildew on cucumber has been successfully controlled for many years through host resistance. However, since the 2004 growing season, host resistance has been effective no longer and, as a result, the control of downy mildew on cucurbits now requires an intensive fungicide programme. Chemical control is not always feasible because of the high costs associated with fungicides and their application. Moreover, the presence of pathogen populations resistant to commonly used fungicides limits the long‐term viability of chemical control. This review summarizes the current knowledge of taxonomy, disease development, virulence, pathogenicity and control of Ps. cubensis. In addition, topics for future research that aim to develop both short‐ and long‐term control measures of cucurbit downy mildew are discussed.Taxonomy: Kingdom Straminipila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Pseudoperonospora; Species Pseudoperonospora cubensis.Disease symptoms: Angular chlorotic lesions bound by leaf veins on the foliage of cucumber. Symptoms vary on different cucurbit species and varieties, specifically in terms of lesion development, shape and size. Infection of cucurbits by Ps. cubensis impacts fruit yield and overall plant health.Infection process: Sporulation on the underside of leaves results in the production of sporangia that are dispersed by wind. On arrival on a susceptible host, sporangia germinate in free water on the leaf surface, producing biflagellate zoospores that swim to and encyst on stomata, where they form germ tubes. An appressorium is produced and forms a penetration hypha, which enters the leaf tissue through the stomata. Hyphae grow through the mesophyll and establish haustoria, specialized structures for the transfer of nutrients and signals between host and pathogen.Control: Management of downy mildew in Europe requires the use of tolerant cucurbit cultivars in conjunction with fungicide applications. In the USA, an aggressive fungicide programme, with sprays every 5–7 days for cucumber and every 7–10 days for other cucurbits, has been necessary to control outbreaks and to prevent crop loss.Useful websites:  http://www.daylab.plp.msu.edu/pseudoperonospora‐cubensis/ (Day Laboratory website with research advances in downy mildew); http://veggies.msu.edu/ (Hausbeck Laboratory website with downy mildew news for growers); http://cdm.ipmpipe.org/ (Cucurbit downy mildew forecasting homepage); http://ipm.msu.edu/downymildew.htm (Downy mildew information for Michigan's vegetable growers).}, number={3}, journal={Molecular Plant Pathology}, publisher={Wiley-Blackwell}, author={SAVORY, ELIZABETH A. and GRANKE, LEAH L. and QUESADA-OCAMPO, LINA M. and VARBANOVA, MARINA and HAUSBECK, MARY K. and BRAD, DAY}, year={2010}, month={Nov}, pages={217–226} }
 @article{vargas_ocampo_céspedes_carreño_gonzález_rojas_zuluaga_myers_fry_jiménez_et al._2009, title={Characterization of Phytophthora infestans Populations in Colombia: First Report of the A2 Mating Type}, volume={99}, DOI={10.1094/phyto-99-1-0082}, abstractNote={ Phytophthora infestans, the causal agent of late blight in crops of the Solanaceae family, is one of the most important plant pathogens in Colombia. Not only are Solanum lycopersicum, and S. tuberosum at risk, but also several other solanaceous hosts (Physalis peruviana, S. betaceum, S. phureja, and S. quitoense) that have recently gained importance as new crops in Colombia may be at risk. Because little is known about the population structure of Phytophthora infestans in Colombia, we report here the phenotypic and molecular characterization of 97 isolates collected from these six different solanaceous plants in Colombia. All the isolates were analyzed for mating type, mitochondrial haplotypes, genotype for several microsatellites, and sequence of the internal transcribed spacer (ITS) region. This characterization identified a single individual of A2 mating type (from Physalis peruviana) for the first time in Colombia. All isolates had an ITS sequence that was at least 97% identical to the consensus sequence. Of the 97 isolates, 96 were mitochondrial haplotype IIa, with the single A2 isolate being Ia. All isolates were invariant for the microsatellites. Additionally, isolates collected from S. tuberosum and P. peruviana (64 isolates) were tested for: aggressiveness on both hosts, genotype for the isozymes (glucose-6-phosphate isomerase and peptidase), and restriction fragment length polymorphism fingerprint pattern as detected by RG57. Isolates from S. tuberosum were preferentially pathogenic on S. tuberosum, and isolates from P. peruviana were preferentially pathogenic on P. peruviana. The population from these two hosts was dominated by a single clonal lineage (59 of 64 individuals assayed), previously identified from Ecuador and Peru as EC-1. This lineage was mating type A1, IIa for mitochondrial DNA, invariant for two microsatellites, and invariant for both isozymes. The remaining four A1 isolates were in lineages very closely related to EC-1 (named EC-1.1, CO-1, and CO-2). The remaining lineage (the A2 mating type) had characteristics of the US-8 lineage (previously identified in Mexico, the United States, and Canada). These results have important epidemiological implications for the production of these two crops in Colombia. }, number={1}, journal={Phytopathology}, publisher={Scientific Societies}, author={Vargas, Angela M. and Ocampo, Lina M. Quesada and Céspedes, Maria Catalina and Carreño, Natalia and González, Adriana and Rojas, Alejandro and Zuluaga, A. Paola and Myers, Kevin and Fry, William E. and Jiménez, Pedro and et al.}, year={2009}, month={Jan}, pages={82–88} }
 @article{bos_chaparro-garcia_quesada-ocampo_gardener_kamoun_2009, title={Distinct Amino Acids of the Phytophthora infestans Effector AVR3a Condition Activation of R3a Hypersensitivity and Suppression of Cell Death}, volume={22}, DOI={10.1094/mpmi-22-3-0269}, abstractNote={ The AVR3a protein of Phytophthora infestans is a polymorphic member of the RXLR class of cytoplasmic effectors with dual functions. AVR3aKI but not AVR3aEM activates innate immunity triggered by the potato resistance protein R3a and is a strong suppressor of the cell-death response induced by INF1 elicitin, a secreted P. infestans protein that has features of pathogen-associated molecular patterns. To gain insights into the molecular basis of AVR3a activities, we performed structure-function analyses of both AVR3a forms. We utilized saturated high-throughput mutant screens to identify amino acids important for R3a activation. Of 6,500 AVR3aEM clones tested, we identified 136 AVR3aEM mutant clones that gained the ability to induce R3a hypersensitivity. Fifteen amino-acid sites were affected in this set of mutant clones. Most of these mutants did not suppress cell death at a level similar to that of AVR3aKI. A similar loss-of-function screen of 4,500 AVR3aKI clones identified only 13 mutants with altered activity. These results point to models in which AVR3a functions by interacting with one or more host proteins and are not consistent with the recognition of AVR3a through an enzymatic activity. The identification of mutants that gain R3a activation but not cell-death suppression activity suggests that distinct amino acids condition the two AVR3a effector activities. }, number={3}, journal={MPMI}, publisher={Scientific Societies}, author={Bos, Jorunn I. B. and Chaparro-Garcia, Angela and Quesada-Ocampo, Lina M. and Gardener, Brian B. McSpadden and Kamoun, Sophien}, year={2009}, month={Mar}, pages={269–281} }
 @article{quesada-ocampo_fulbright_hausbeck_2009, title={Susceptibility of Fraser Fir to Phytophthora capsici}, volume={93}, DOI={10.1094/pdis-93-2-0135}, abstractNote={ Phytophthora cinnamomi, P. drechsleri, P. citricola, and P. cactorum limit Fraser fir production, whereas P. capsici affects Solanaceous, Cucurbitaceous, and Fabaceous crops. Some vegetable growers in Michigan plant conifers for the Christmas tree market in fields infested with P. capsici. To determine the susceptibility of Fraser fir to P. capsici, stems (no wound or 1- or 3-mm-diameter wound) or roots (2 or 4 g of infested millet seed or 2 or 5 × 103 zoospores/ml of a zoospore suspension) of seedlings were inoculated with each of four P. capsici isolates and incubated in growth chambers (20 or 25°C). In addition, Fraser fir seedlings were planted in two commercial fields naturally infested with P. capsici. All P. capsici isolates tested incited disease in the seedlings regardless of incubation temperature or inoculation method. Seedlings (72%) planted in P. capsici–infested fields developed disease symptoms and died. Most of the P. capsici isolates obtained from the Fraser fir seedlings infected while in the field were recovered from root tissue. Identification was confirmed by species-specific direct colony polymerase chain reaction. The pathogen was successfully recovered from stems of all stem-inoculated seedlings, and from roots and stems of all root-inoculated seedlings; the phenotype of the recovered isolate matched the phenotype of the inoculum. This study suggests that planting Fraser fir in fields infested with P. capsici could result in infection and that adjustments in current rotational schemes are needed. }, number={2}, journal={Plant Disease}, publisher={Scientific Societies}, author={Quesada-Ocampo, L. M. and Fulbright, D. W. and Hausbeck, M. K.}, year={2009}, month={Feb}, pages={135–141} }
 @article{matute_quesada-ocampo_rauscher_mcewen_2008, title={Evidence for Positive Selection in Putative Virulence Factors within the Paracoccidioides brasiliensis Species Complex}, volume={2}, DOI={10.1371/journal.pntd.0000296}, abstractNote={Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis, the most important prevalent systemic mycosis in Latin America. Recently, the existence of three genetically isolated groups in P. brasiliensis was demonstrated, enabling comparative studies of molecular evolution among P. brasiliensis lineages. Thirty-two gene sequences coding for putative virulence factors were analyzed to determine whether they were under positive selection. Our maximum likelihood–based approach yielded evidence for selection in 12 genes that are involved in different cellular processes. An in-depth analysis of four of these genes showed them to be either antigenic or involved in pathogenesis. Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection. The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection. Our results are consistent with the more general observations that selective constraints are variable across the genome, and that even in the genes under positive selection, only a few sites are altered. We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.}, number={9}, journal={PLoS Negl Trop Dis}, publisher={Public Library of Science (PLoS)}, author={Matute, Daniel R. and Quesada-Ocampo, Lina M. and Rauscher, Jason T. and McEwen, Juan G.}, editor={Taylor, John W.Editor}, year={2008}, month={Sep}, pages={e296} }
 @article{somers_lópez_quesada-ocampo_bohórquez_duque_vargas_tohme_verdier_2007, title={Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta}, volume={50}, DOI={10.1139/g07-087}, abstractNote={Cassava ( Manihot esculenta Crantz) is a major root crop widely grown in the tropics. Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in Latin America and Africa resulting in significant losses. The preferred control method is the use of resistant genotypes. Mapping expressed sequence tags (ESTs) and determining their co-localization with quantitative trait loci (QTLs) may give additional evidence of the role of the corresponding genes in resistance or defense. Twenty-one EST-derived simple sequence repeats (SSRs) were mapped in 16 linkage groups. ESTs showing similarities with candidate resistance genes or defense genes were also mapped using strategies such as restriction fragment length polymorphisms, cleaved amplified polymorphic sequences, and allele-specific primers. In total, 10 defense-related genes and 2 bacterial artificial chromosomes (BACs) containing resistance gene candidates (RGCs) were mapped in 11 linkage groups. Two new QTLs associated with resistance to Xam strains CIO121 and CIO151 were detected in linkage groups A and U, respectively. The QTL in linkage group U explained 61.6% of the phenotypic variance and was associated with an RGC-containing BAC. No correlation was found between the new EST-derived SSRs or other mapped ESTs and the new or previously reported QTLs.}, number={12}, journal={Genome}, publisher={Canadian Science Publishing}, author={Somers, Daryl and López, Camilo E. and Quesada-Ocampo, Lina M. and Bohórquez, Adriana and Duque, Myriam Cristina and Vargas, Jaime and Tohme, Joe and Verdier, Valérie}, year={2007}, pages={1078–1088} }