@article{roberts_thomas_salmon_cubeta_stapelmann_gilger_2024, title={Cold atmospheric plasma inactivates<i> Aspergillus</i><i> flavus</i> and Fusarium keratoplasticum biofilms and conidia in vitro}, volume={73}, ISSN={["1473-5644"]}, url={https://doi.org/10.1099/jmm.0.001858}, DOI={10.1099/jmm.0.001858}, abstractNote={Introduction. Aspergillus flavus and Fusarium keratoplasticum are common causative pathogens of fungal keratitis (FK), a severe corneal disease associated with significant morbidity and vision loss. Escalating incidence of antifungal resistance to available antifungal drugs poses a major challenge to FK treatment. Cold atmospheric plasma (CAP) is a pioneering nonpharmacologic antimicrobial intervention that has demonstrated potential as a broad-spectrum antifungal treatment. Gap statement. Previous research highlights biofilm-associated resistance as a critical barrier to effective FK treatment. Although CAP has shown promise against various fungal infections, its efficacy against biofilm and conidial forms of FK pathogens remains inadequately explored. Aim. This study aims to investigate the antifungal efficacy of CAP against clinical fungal keratitis isolates of A. flavus and F. keratoplasticum in vitro . Methodology. Power parameters (22–27 kV pp , 300–400 Hz and 20–80 mA) of a dielectric barrier discharge CAP device were optimized for inactivation of A. flavus biofilms. Optimal applied voltage and total current were applied to F. keratoplasticum biofilms and conidial suspensions of A. flavus and F. keratoplasticum . The antifungal effect of CAP treatment was investigated by evaluating fungal viability through means of metabolic activity, c.f.u. enumeration (c.f.u. ml −1 ) and biofilm formation. Results. For both fungal species, CAP exhibited strong time-dependent inactivation, achieving greater than 80 % reduction in metabolic activity and c.f.u. ml −1 within 300 s or less, and complete inhibition after 600 s of treatment. Conclusion. Our findings indicate that CAP is a promising broad-spectrum antifungal intervention. CAP treatment effectively reduces fungal viability in both biofilm and conidial suspension cultures of A. flavus and F. keratoplasticum , suggesting its potential as an alternative treatment strategy for fungal keratitis.}, number={7}, journal={JOURNAL OF MEDICAL MICROBIOLOGY}, author={Roberts, Darby and Thomas, Jonathan and Salmon, Jacklyn and Cubeta, Marc A. and Stapelmann, Katharina and Gilger, Brian C.}, year={2024} }
 @article{french_chukwuma_linshitz_namba_duckworth_cubeta_baars_2024, title={Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont <i>Pyrenophora biseptata</i>}, volume={1}, ISSN={["1758-2229"]}, url={https://doi.org/10.1111/1758-2229.13234}, DOI={10.1111/1758-2229.13234}, abstractNote={AbstractWe investigated the ability of four plant and soil‐associated fungi to modify or degrade siderophore structures leading to reduced siderophore iron‐affinity in iron‐limited and iron‐replete cultures. Pyrenophora biseptata, a melanized fungus from wheat roots, was effective in inactivating siderophore iron‐chelating moieties. In the supernatant solution, the tris‐hydroxamate siderophore desferrioxamine B (DFOB) underwent a stepwise reduction of the three hydroxamate groups in DFOB to amides leading to a progressive loss in iron affinity. A mechanism is suggested based on the formation of transient ferrous iron followed by reduction of the siderophore hydroxamate groups during fungal high‐affinity reductive iron uptake. P. biseptata also produced its own tris‐hydroxamate siderophores (neocoprogen I and II, coprogen and dimerum acid) in iron‐limited media and we observed loss of hydroxamate chelating groups during incubation in a manner analogous to DFOB. A redox‐based reaction was also involved with the tris‐catecholate siderophore protochelin in which oxidation of the catechol groups to quinones was observed. The new siderophore inactivating activity of the wheat symbiont P. biseptata is potentially widespread among fungi with implications for the availability of iron to plants and the surrounding microbiome in siderophore‐rich environments.}, journal={ENVIRONMENTAL MICROBIOLOGY REPORTS}, author={French, Katie S. and Chukwuma, Emmanuel and Linshitz, Ilan and Namba, Kosuke and Duckworth, Owen W. and Cubeta, Marc A. and Baars, Oliver}, year={2024}, month={Jan} }
 @article{becker_cubeta_2024, title={Multigenerational Drought Reveals a Stable Wheat Seed Fungal Community}, volume={6}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-08-23-0083-R}, abstractNote={Wheat (Triticum spp.) is a staple food crop, providing a fifth of the world’s protein and caloric needs. Our research examines the impact of multi generation post-flowering drought stress on the wheat seed endophytic fungal community. Understanding how wheat seed fungal communities respond to drought stress over several generations can improve our knowledge of legacy drought stress. In this manuscript, we aim to identify seed associated fungi that play critical roles within the wheat seed under drought stress conditions. We examined the endophytic seed fungal communities of three winter wheat cultivars, Catawba, Shirley, and USG 3640. Moderate drought was imposed on a subset of plants immediately after flowering, with plants relieved from drought stress after one week. Seeds harvested from generation 1 were planted for a second generation of drought experiments. When examining post-flowering drought impact on wheat physiology, drought-exposed plants consistently exhibited lower daily transpiration rates, chlorophyll-a values, and seed yield compared to control plants, indicating that drought implementation was successful. ITS1 metabarcoding revealed that wheat seed fungal community species richness decreased during post-anthesis drought stress across both generations. We also observed that generation accounted for variation in fungal species richness and community structure, independent of drought treatment. The most abundant taxa recovered across all cultivars, treatments, and generations included Cladosporium, Penicillium, Alternaria, and Epicoccum. These results support our hypothesis that post-anthesis drought shapes the wheat seed fungal community.}, journal={PHYTOBIOMES JOURNAL}, author={Becker, Lindsey E. and Cubeta, Marc A.}, year={2024}, month={Jun} }
 @article{doydora_baars_cubeta_duckworth_urbieta_castro_2024, title={Using Manganese Oxidizing Fungi to Recover Metals from Electronic Waste}, volume={14}, ISSN={["2075-163X"]}, url={https://www.mdpi.com/2075-163X/14/1/111}, DOI={10.3390/min14010111}, abstractNote={Discarded electronic materials (e-waste) contain economically valuable metals that can be hazardous to people and the environment. Current e-waste recycling approaches involve either energy-intensive smelting or bioleaching processes that capture metals in their dissolved forms. Our study aimed to use Mn oxidizing fungi for recovering metals from e-waste that could potentially transform recycled metals directly into solid forms. We hypothesized that Mn oxidizing fungi can extract metals through chelation by siderophores and subsequent metal (or metal-chelate) adsorption to Mn oxides produced by fungi. Pure cultures of the three fungal species examined were grown on solidified Leptothrix medium with or without ground lithium ion batteries and incubated under ambient room temperature. The results showed Mn and Co were recovered at the highest concentrations of 8.45% and 1.75%, respectively, when grown with Paraconiothyrium brasiliensis, whereas the greatest concentration of Cu was extracted by Paraphaeosphaeria sporulosa at 20.6% per weight of e-waste-derived metals. Although metal-siderophore complexes were detected in the fungal growth medium, metal speciation data suggested that these complexes only occurred with Fe. This observation suggests that reactions other than complexation with siderophores likely solubilized e-waste metals. Elemental mapping, particularly of P. brasiliensis structures, showed a close association between Mn and Co, suggesting potential adsorption or (co)precipitation of these two metals near fungal mycelium. These findings provide experimental evidence for the potential use of Mn oxidizing fungi in recycling and transforming e-waste metals into solid biominerals. However, optimizing fungal growth conditions with e-waste is needed to improve the efficiency of metal recovery.}, number={1}, journal={MINERALS}, author={Doydora, Sarah A. and Baars, Oliver and Cubeta, Marc A. and Duckworth, Owen W. and Urbieta, Maria Sofia and Castro, Laura}, year={2024}, month={Jan} }
 @article{weaver_alexander_cubeta_knappe_aziz_2023, title={Degradation of imidacloprid by Phanerodontia chrysosporium on wood chips for stormwater treatment}, volume={9}, ISSN={["2053-1419"]}, url={https://doi.org/10.1039/D3EW00545C}, DOI={10.1039/d3ew00545c}, abstractNote={The white-rot fungus Phanerodontia chrysosporium degraded more than 50% of imidacloprid in synthetic stormwater in one week, demonstrating the potential of fungal bioremediation for improved contaminant removal in stormwater infrastructure.}, number={12}, journal={ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY}, author={Weaver, Leah M. M. and Alexander, Nancy Lee and Cubeta, Marc A. and Knappe, Detlef R. U. and Aziz, Tarek N.}, year={2023}, month={Nov}, pages={3333–3343} }
 @article{stephens_gannon_thiessen_cubeta_kerns_2023, title={In Vitro Fungicide Sensitivity and Effect of Organic Matter Concentration on Fungicide Bioavailability in Take-All Root Rot Pathogens Isolated from North Carolina}, volume={24}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-08-22-0072-RS}, abstractNote={ Take-all root rot (TARR) of ultradwarf bermudagrass is caused by Gaeumannomyces graminis (Gg), Gaeumannomyces graminicola (Ggram), Candidacolonium cynodontis (Cc), and Magnaporthiopsis cynodontis (Mc). Multiple pathogens have recently been associated with this disease, and biological parameters such as fungicide sensitivity have not been explored in ultradwarf bermudagrass. Although fungicides are commonly used to mitigate disease development, high organic matter present in the turfgrass system could limit the bioavailability of fungicides. Fungicide bioavailability can be influenced by organic matter concentration, and the physicochemical properties of fungicides could provide insight into their binding affinity. However, the influence of organic matter content on fungicide bioavailability has not been investigated. Therefore, the in vitro sensitivity of Gg, Ggram, Cc, and Mc to 14 different fungicides across three chemical classes was determined. An in vitro bioavailability assay was developed using three fungicides and three organic matter concentrations. Generally, demethylation inhibitor and quinone outside inhibitor fungicides provided the greatest reduction in mycelial growth, whereas succinate dehydrogenase inhibitors did not reduce mycelial growth. These data can serve as a foundation for TARR pathogen sensitivity to inform in vitro fungicide sensitivity studies and field efficacy trials. Pyraclostrobin and propiconazole have a high affinity to bind to organic matter, which was evident as more fungicide was required to inhibit Gg growth as organic matter concentration increased. This was not observed when evaluating azoxystrobin, which has a lower binding affinity. Understanding how TARR pathogens respond to fungicide in vitro and how organic matter concentration affects in vitro sensitivity will improve fungicide selection for management of TARR. }, number={2}, journal={PLANT HEALTH PROGRESS}, author={Stephens, Cameron M. and Gannon, Travis W. and Thiessen, Lindsey D. and Cubeta, Marc A. and Kerns, James P.}, year={2023}, month={Jul}, pages={162–170} }
 @article{stephens_gannon_cubeta_kerns_2024, title={Influence of fungicide selection and application timing on take-all root rot management under field and greenhouse conditions}, volume={10}, ISSN={["2374-3832"]}, DOI={10.1002/cft2.20261}, abstractNote={Abstract Take‐all root rot (TARR) is a detrimental disease of ultradwarf bermudagrass ( Cynodon dactylon × Cynodon transvaalensis ; UDB) putting greens frequently diagnosed where warm‐season grasses are grown. Since this disease is largely aggregated and variable under field conditions, field research is difficult and often yields inconsistent results. Multiple pathogens have only recently been associated with this disease, so practical management solutions such as fungicide efficacy and fungicide application timing have not been thoroughly investigated. Therefore, the objectives of this research were to determine the influence of fungicide selection and fungicide application timing on take‐all root rot management under field and greenhouse conditions. In general, fungicides from the quinone outside inhibitor and/or demethylation inhibitor chemical classes provided the greatest reduction in take‐all root rot severity. Fungicide applications that were made when soil temperatures were between 77–86°F provided the greatest disease suppression. The in vivo greenhouse method developed in this research proved to be an efficient and consistent method to evaluate management practices such as fungicide efficacy on take‐all root rot. This research improves our understanding of fungicide efficacy and fungicide application timing for take‐all root rot management on ultradwarf bermudagrass.}, number={1}, journal={CROP FORAGE & TURFGRASS MANAGEMENT}, author={Stephens, Cameron M. and Gannon, Travis W. and Cubeta, Marc A. and Kerns, James P.}, year={2024}, month={Jun} }
 @article{swenie_looney_ke_rojas_cubeta_langer_vilgalys_matheny_2023, title={PacBio high-throughput multi-locus sequencing reveals high genetic diversity in mushroom-forming fungi}, volume={10}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.13885}, abstractNote={AbstractMulti‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genes rpb1, rpb2 and tef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi.}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Swenie, Rachel A. and Looney, Brian P. and Ke, Yi-Hong and Rojas, Jorge A. and Cubeta, Marc A. and Langer, Gitta J. and Vilgalys, Rytas and Matheny, Patrick B.}, year={2023}, month={Oct} }
 @article{roberts_salmon_cubeta_gilger_2023, title={Phase-Dependent Differential In Vitro and Ex Vivo Susceptibility of Aspergillus flavus and Fusarium keratoplasticum to Azole Antifungals}, volume={9}, ISSN={2309-608X}, url={http://dx.doi.org/10.3390/jof9100966}, DOI={10.3390/jof9100966}, abstractNote={Fungal keratitis (FK) is an invasive infection of the cornea primarily associated with Aspergillus and Fusarium species. FK is treated empirically with a limited selection of topical antifungals with varying levels of success. Though clinical infections are typically characterized by a dense network of mature mycelium, traditional models used to test antifungal susceptibility of FK isolates exclusively evaluate susceptibility in fungal cultures derived from asexual spores known as conidia. The purpose of this study was to characterize differences in fungal response when topical antifungal treatment is initiated at progressive phases of fungal development. We compared the efficacy of voriconazole and luliconazole against in vitro cultures of A. flavus and F. keratoplasticum at 0, 24, and 48 h of fungal development. A porcine cadaver corneal model was used to compare antifungal efficacy of voriconazole and luliconazole in ex vivo tissue cultures of A. flavus and F. keratoplasticum at 0, 24, and 48 h of fungal development. Our results demonstrate phase-dependent susceptibility of both A. flavus and F. keratoplasticum to both azoles in vitro as well as ex vivo. We conclude that traditional antifungal susceptibility testing with conidial suspensions does not correlate with fungal susceptibility in cultures of a more advanced developmental phase. A revised method of antifungal susceptibility testing that evaluates hyphal susceptibility may better predict fungal response in the clinical setting where treatment is often delayed until days after the initial insult.}, number={10}, journal={Journal of Fungi}, publisher={MDPI AG}, author={Roberts, Darby and Salmon, Jacklyn and Cubeta, Marc A. and Gilger, Brian C.}, year={2023}, month={Sep}, pages={966} }
 @article{rogers_koehler_crouch_cubeta_leblanc_2022, title={Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata}, volume={22}, ISSN={["2730-7182"]}, DOI={10.1186/s12862-022-02035-4}, abstractNote={AbstractBackgroundBoxwood blight disease caused byCalonectria henricotiaeandC. pseudonaviculatais of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity ofC. henricotiaeandC. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution inC. henricotiae,C. pseudonaviculataand 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles.ResultsA total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the sixCalonectriaspecies,C. henricotiaeandC. pseudonaviculatawere the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic speciesCalonectria multiphialidicaandC. naviculata, two of the closest known relatives ofC. henricotiaeandC. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families.ConclusionsOur results provide novel insight into gene family evolution withinC. henricotiaeandC. pseudonaviculataand suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae.}, number={1}, journal={BMC ECOLOGY AND EVOLUTION}, author={Rogers, Layne W. and Koehler, Alyssa M. and Crouch, Jo Anne and Cubeta, Marc A. and LeBlanc, Nicholas R.}, year={2022}, month={Jun} }
 @article{nowicki_hadziabdic_trigiano_boggess_kanetis_wadl_ojiambo_cubeta_spring_thines_et al._2021, title={"Jumping Jack ": Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past}, volume={12}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2021.686759}, abstractNote={Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host–pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Nowicki, Marcin and Hadziabdic, Denita and Trigiano, Robert N. and Boggess, Sarah L. and Kanetis, Loukas and Wadl, Phillip A. and Ojiambo, Peter S. and Cubeta, Marc A. and Spring, Otmar and Thines, Marco and et al.}, year={2021}, month={Jul} }
 @article{stephens_gannon_cubeta_sit_kerns_2022, title={Characterization and Aggressiveness of Take-All Root Rot Pathogens Isolated from Symptomatic Bermudagrass Putting Greens}, volume={112}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-05-21-0215-R}, abstractNote={ Take-all root rot is a disease of ultradwarf bermudagrass putting greens caused by Gaeumannomyces graminis (Gg), Gaeumannomyces sp. (Gx), Gaeumannomyces graminicola (Ggram), Candidacolonium cynodontis (Cc), and Magnaporthiopsis cynodontis (Mc). Many etiological and epidemiological components of this disease remain unknown. Improving pathogen identification and our understanding of the aggressiveness of these pathogens along with growth at different temperatures will advance our knowledge of disease development to optimize management strategies. Take-all root rot pathogens were isolated from symptomatic bermudagrass root and stolon pieces from 16 different golf courses. Isolates of Gg, Gx, Ggram, Cc, and Mc were used to inoculate ‘Champion’ bermudagrass in an in planta aggressiveness assay. Each pathogen was also evaluated at 10, 15, 20, 25, 30, and 35°C to determine growth temperature optima. Infected plant tissue was used to develop a real-time PCR high-resolution melt assay for pathogen detection. This assay was able to differentiate each pathogen directly from infected plant tissue using a single primer pair. In general, Ggram, Gg, and Gx were the most aggressive while Cc and Mc exhibited moderate aggressiveness. Pathogens were more aggressive when incubated at 30°C compared with 20°C. While they grew optimally between 24.4 and 27.8°C, pathogens exhibited limited growth at 35°C and no growth at 10°C. These data provide important information on this disease and its causal agents that may improve take-all root rot management. }, number={4}, journal={PHYTOPATHOLOGY}, author={Stephens, Cameron M. and Gannon, Travis W. and Cubeta, Marc A. and Sit, Tim L. and Kerns, James P.}, year={2022}, month={Apr}, pages={811–819} }
 @article{stalpers_redhead_may_rossman_crouch_cubeta_dai_kirschner_langer_larsson_et al._2021, title={Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use}, volume={12}, ISSN={["2210-6359"]}, DOI={10.1186/s43008-021-00061-3}, abstractNote={AbstractWith the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.}, number={1}, journal={IMA FUNGUS}, author={Stalpers, Joost A. and Redhead, Scott A. and May, Tom W. and Rossman, Amy Y. and Crouch, Jo Anne and Cubeta, Marc A. and Dai, Yu-Cheng and Kirschner, Roland and Langer, Gitta Jutta and Larsson, Karl-Henrik and et al.}, year={2021}, month={Aug} }
 @article{yow_zhang_bansal_eacker_sullivan_liachko_cubeta_rollins_ashrafi_2021, title={Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type}, volume={11}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkaa052}, DOI={10.1093/g3journal/jkaa052}, abstractNote={Abstract
               Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was characterized. Biotrophic effectors allow the pathogen to avoid recognition by the host plant and evade or mitigate host defense responses during the early stages of fruit infection. Following locule colonization, necrotizing effectors promote the mummification of host tissues. Potential biotrophic effectors utilized by Mvc include chorismate mutase for reducing host salicylate and necrotrophic effectors include necrosis-inducing proteins and hydrolytic enzymes for macerating host tissue. The MAT locus sequences indicate the potential for homothallism in the reference genome, but a deletion allele of the MAT locus, characterized in a second isolate, indicates heterothallism. Further research is needed to verify the roles of individual effectors in virulence and to determine the role of the MAT locus in outcrossing and population genotypic diversity.}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Yow, Ashley G. and Zhang, Yucheng and Bansal, Kamaldeep and Eacker, Stephen M. and Sullivan, Shawn and Liachko, Ivan and Cubeta, Marc A. and Rollins, Jeffrey A. and Ashrafi, Hamid}, editor={Baltrus, DEditor}, year={2021}, month={Feb} }
 @article{leblanc_cubeta_crouch_2021, title={Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood}, volume={111}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-06-20-0219-FI}, abstractNote={ Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species Calonectria pseudonaviculata has remained genetically isolated from its European-limited sister species C. henricotiae, while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 C. pseudonaviculata isolates from four continents and 1,017 SNPs in 13 C. henricotiae isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in C. pseudonaviculata identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two C. pseudonaviculata genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation. }, number={1}, journal={PHYTOPATHOLOGY}, author={LeBlanc, Nicholas and Cubeta, Marc A. and Crouch, Jo Anne}, year={2021}, month={Jan}, pages={184–193} }
 @article{flemming_phillips_shea_bolton_lincoln_green_mast_cubeta_2020, title={Using Digital Natural History Collections in K-12 STEM Education}, volume={45}, ISSN={["2051-6169"]}, DOI={10.1080/10598650.2020.1833296}, abstractNote={ABSTRACT Natural history collections contain billions of specimens which are used to inform our understanding of the biodiversity of our planet. Digitized natural history collections (dNHCs) provide an accessible resource for multiple audiences, including K-12 teachers. The incorporation of dNHCs in K-12 classrooms provides an opportunity to engage students in authentic and practical science experiences. More importantly, through collaboration with museum educators the use of dNHCs can address some of the challenges K-12 teachers face when addressing the Next Generation Science Standards. Using primary data sources will ensure students understand the natural world through the perspective of scientific practices that involve data analyses, structured experiential and inquiry-based learning, and constructing explanations in a hypothesis-testing framework.}, number={4}, journal={JOURNAL OF MUSEUM EDUCATION}, author={Flemming, Adania and Phillips, Molly and Shea, Elizabeth K. and Bolton, Amy and Lincoln, Cynthia and Green, Kathryn and Mast, Austin and Cubeta, Marc A.}, year={2020}, month={Oct}, pages={450–461} }
 @article{green_roller_cubeta_2019, title={A Plethora of Fungi: Teaching a Middle School Unit on Fungi}, volume={56}, ISSN={1940-1302}, url={https://www.tandfonline.com/loi/vsca20.}, DOI={10.1080/00368121.2019.1682961}, abstractNote={Abstract While fungi play a vital role in Earth's ecosystems, they are not highlighted in the Next Generation Science Standards (NGSS). This article contains a unit plan to introduce students to the fungal kingdom, characteristics of fungi, and their role as decomposers. The unit plan is written in a 5E model format and can be adjusted for any type of lesson planning format. Students explore fungi through hands-on activities, a jigsaw activity that makes use of collaborative learning, and analysis of case studies. Teachers can use this unit without a strong background in mycology, the study of fungi, or costly materials. A summative assessment is included at the end of the unit plan.}, number={2}, journal={Science Activities}, author={Green, K.E. and Roller, C. and Cubeta, M.A.}, year={2019}, pages={52–62} }
 @article{koehler_larkin_rogers_carbone_cubeta_shew_2019, title={Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina}, volume={111}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/00275514.2019.1584503}, DOI={10.1080/00275514.2019.1584503}, abstractNote={ABSTRACT Stevia (Stevia rebaudiana) is an emerging perennial crop in the southeastern United States. A Septoria leaf spot disease of stevia was first identified on field plantings in Japan in 1978. The pathogen was named Septoria steviae based on a morphological characterization. In 2015, a species of Septoria with morphological characters of S. steviae was isolated from field and greenhouse-grown stevia plants with leaf spot symptoms in North Carolina. In this study, 12 isolates obtained from diseased stevia plants in 2015 and 2016 were characterized and compared with reference strains of S. steviae. Comparisons were based on conidial and pycnidial morphology and multilocus sequence analysis of actin (ACT), β-tubulin (BT), calmodulin (CAL), nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS), nuc rDNA 28S subunit (28S), RNA polymerase II second largest subunit (RPB2), and translation elongation factor-1α (TEF1). Measurements of conidia and pycnidia from symptomatic field leaves and 12 pure cultures grown on nutrient medium were consistent with those previously reported for ex-type strains of S. steviae. North Carolina strains formed a well-supported monophyletic group with ex-type strains of S. steviae. This study represents the first genetic characterization of S. steviae in the United States and provides an experimental framework to elucidate the genetic diversity and disease ecology of field populations of S. steviae.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Koehler, Alyssa M. and Larkin, Maximo T. and Rogers, Layne W. and Carbone, Ignazio and Cubeta, Marc A. and Shew, H. David}, year={2019}, month={Apr}, pages={456–465} }
 @article{cullen_jacob_cornish_vanderschel_cotter_cubeta_carbone_gilger_2019, title={Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0214214}, DOI={10.1371/journal.pone.0214214}, abstractNote={Morphological characterization and multi-locus DNA sequence analysis of fungal isolates obtained from 32 clinical cases of equine fungal keratitis (FK) was performed to identify species and determine associations with antifungal susceptibility, response to therapy and clinical outcome. Two species of Aspergillus (A. flavus and A. fumigatus) and three species of Fusarium (F. falciforme, F. keratoplasticum, and F. proliferatum) were the most common fungi isolated and identified from FK horses. Most (91%) equine FK Fusarium nested within the Fusarium solani species complex (FSSC) with nine genetically diverse strains/lineages, while 83% of equine FK Aspergillus nested within the A. flavus clade with three genetically diverse lineages. Fungal species and evolutionary lineage were not associated with clinical outcome. However, species of equine FK Fusarium were more likely (p = 0.045) to be associated with stromal keratitis. Species of Aspergillus were more susceptible to voriconazole and terbinafine than species of Fusarium, while species of Fusarium were more susceptible to thiabendazole than species of Aspergillus. At the species level, A. fumigatus and A. flavus were more susceptible to voriconazole and terbinafine than F. falciforme. Natamycin susceptibility was higher for F. falciforme and A. fumigatus compared to A. flavus. Furthermore, F. falciforme was more susceptible to thiabendazole than A. flavus and A. fumigatus. These observed associations of antifungal sensitivity to natamycin, terbinafine, and thiabendazole demonstrate the importance of fungal identification to the species rather than genus level. The results of this study suggest that treatment of equine FK with antifungal agents requires accurate fungal species identification.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Cullen, Megan and Jacob, Megan E. and Cornish, Vicki and VanderSchel, Ian Q. and Cotter, Henry Van T. and Cubeta, Marc A. and Carbone, Ignazio and Gilger, Brian C.}, editor={Kniemeyer, OlafEditor}, year={2019}, month={Mar}, pages={e0214214} }
 @article{salgado-salazar_shiskoff_leblanc_ismaiel_collins_cubeta_crouch_2019, title={Coccinonectria pachysandricola, Causal Agent of a New Foliar Blight Disease of Sarcococca hookeriana}, volume={103}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-09-18-1676-RE}, DOI={10.1094/PDIS-09-18-1676-RE}, abstractNote={ Woody plants of the Buxaceae, including species of Buxus, Pachysandra, and Sarcococca, are widely grown evergreen shrubs and groundcovers. Severe leaf spot symptoms were observed on S. hookeriana at the U.S. National Arboretum in Washington, DC, in 2016. Affected plants were growing adjacent to P. terminalis exhibiting Volutella blight symptoms. Fungi isolated from both hosts were identical based on morphology and multilocus phylogenetic analysis and were identified as Coccinonectria pachysandricola (Nectriaceae, Hypocreales), causal agent of Volutella blight of Pachysandra species. Pathogenicity tests established that Co. pachysandricola isolated from both hosts caused disease symptoms on P. terminalis and S. hookeriana, but not on B. sempervirens. Artificial inoculations with Pseudonectria foliicola, causal agent of Volutella blight of B. sempervirens, did not result in disease on P. terminalis or S. hookeriana. Wounding enhanced infection by Co. pachysandricola and Ps. foliicola on all hosts tested but was not required for disease development. Genome assemblies were generated for the Buxaceae pathogens that cause Volutella diseases: Co. pachysandricola, Ps. buxi, and Ps. foliicola; these ranged in size from 25.7 to 28.5 Mb. To our knowledge, this foliar blight of S. hookeriana represents a new disease for this host and is capable of causing considerable damage to infected plants. }, number={6}, journal={Plant Disease}, publisher={Scientific Societies}, author={Salgado-Salazar, Catalina and Shiskoff, Nina and LeBlanc, Nicholas and Ismaiel, Adnan A. and Collins, Maxton and Cubeta, Marc A. and Crouch, Jo Anne}, year={2019}, month={Jun}, pages={1337–1346} }
 @article{lookabaugh_kerns_cubeta_shew_2018, title={Fitness Attributes of Pythium aphanidermatum with Dual Resistance to Mefenoxam and Fenamidone}, volume={102}, ISSN={0191-2917}, url={http://dx.doi.org/10.1094/PDIS-01-18-0043-RE}, DOI={10.1094/PDIS-01-18-0043-RE}, abstractNote={ Pythium aphanidermatum is the predominant species causing Pythium root rot on commercially grown poinsettias in North Carolina. Resistance to mefenoxam is common in populations of P. aphanidermatum but resistance to fenamidone and other quinone outside inhibitor fungicides has only just been reported in greenhouse floriculture crops. The in vitro sensitivity to the label rate of mefenoxam (17.6 μl active ingredient [a.i.]/ml) and fenamidone (488 μl a.i./ml) was determined for 96 isolates of P. aphanidermatum. Isolates were assigned to four fungicide phenotypes: mefenoxam-sensitive/fenamidone-sensitive (MefS, FenS), mefenoxam-sensitive/fenamidone-insensitive (MefS, FenR), mefenoxam-insensitive/fenamidone-sensitive (MefR, FenS), and mefenoxam-insensitive/fenamidone-insensitive (MefR, FenR). In all, 58% of isolates were insensitive to one (MefR, FenS = 36% and MefS, FenR = 16%) or both fungicides (MefR, FenR = 6%). A single point mutation in the cytochrome b gene (G143A) was identified in fenamidone-insensitive isolates. Mycelial growth rate at three temperatures (20, 25, and 30°C), in vitro oospore production, and aggressiveness on poinsettia were evaluated to assess relative fitness of sensitive and insensitive isolates. Isolates with dual insensitivity to mefenoxam and fenamidone had reduced radial hyphal growth at 30°C and produced fewer oospores than isolates sensitive to one or both fungicides. Isolates sensitive to both fungicides produced greater numbers of oospores. Aggressiveness on poinsettia varied by isolate but fungicide phenotype was not a good predictor of aggressiveness. These results suggest that populations of P. aphanidermatum with dual resistance to mefenoxam and fenamidone may be less fit than sensitive populations under our imposed experimental conditions but populations of P. aphanidermatum should continue to be monitored in poinsettia production systems for mefenoxam and fenamidone insensitivity. }, number={10}, journal={Plant Disease}, publisher={Scientific Societies}, author={Lookabaugh, E. C. and Kerns, J. P. and Cubeta, M. A. and Shew, B. B.}, year={2018}, month={Oct}, pages={1938–1943} }
 @article{miller_shishkoff_cubeta_2018, title={Thermal sensitivity of Calonectria henricotiae and Calonectria pseudonaviculata conidia and microsclerotia}, volume={110}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/00275514.2018.1465778}, DOI={10.1080/00275514.2018.1465778}, abstractNote={ABSTRACT Knowledge of the thermal sensitivity of conidia and microsclerotia is useful for developing plant disease management approaches that deploy heat to inactivate infectious vegetative propagules of fungal pathogens. For boxwood blight disease, heat treatment of cuttings that harbor conidia and microsclerotia would provide a useful management tool for suppressing the pathogenic activity of Calonectria pseudonaviculata (present in the United States) and C. henricotiae (a quarantine pathogen not present in the United States). In this study, we investigated the thermal sensitivity of conidia and microsclerotia of the boxwood blight pathogens C. henricotiae and C. pseudonaviculata treated in water at 45, 47.5, 50, 52.5, and 55 C. For conidia, as time of exposure increased at each temperature, the proportion of germinated conidia decreased. The predicted time required to inactivate 90% of C. pseudonaviculata conidia (LD90) decreased as water temperature increased from 45 to 55 C and ranged from 35.4 to 5.6 min, respectively. Inactivation of conidia was dependent on isolate, species of Calonectria, and length of exposure at each temperature tested. Microsclerotia of C. henricotiae and C. pseudonaviculata displayed reduced germination with increasing exposure and higher temperatures of hot water. Microsclerotia of C. henricotiae were significantly more resistant to heat treatment than C. pseudonaviculata at 47.5 and 50 C, whereas microsclerotia of both species were rapidly killed at 55 C.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Miller, Megan E. and Shishkoff, Nina and Cubeta, Marc A.}, year={2018}, month={May}, pages={546–558} }
 @inbook{cubeta_mozley-standridge_porter_2017, place={Boca Raton. FL}, edition={3rd}, title={Non-Oomycota Zoosporic Plant Pathogens}, booktitle={Plant Pathology Concepts and Laboratory Exercises}, publisher={CRC Press}, author={Cubeta, M.A. and Mozley-Standridge, S.E. and Porter, D.}, editor={Trigiano, R. and Ownley, BonnieEditors}, year={2017}, pages={155–174} }
 @article{duckworth_andrews_cubeta_grunden_ojiambo_2017, title={Revisiting Graduate Student Training to Address Agricultural and Environmental Societal Challenges}, volume={2}, ISSN={2471-9625}, url={http://dx.doi.org/10.2134/ael2017.06.0019}, DOI={10.2134/ael2017.06.0019}, abstractNote={Core Ideas
Society is faced with daunting environmental and agricultural challenges.
There is a pressing need for multidisciplinary teams of collaborative scientists.
Novel graduate educational models may be needed to train students to address grand challenges.
An example of illustrating the model through microbiome science of plants and soil is presented.
Society and the higher education system are faced with daunting challenges associated with supplying food, energy, and water to a growing population while maintaining environmental quality and preserving natural resources. Too often, the higher education system does not facilitate collaborative immersion required to foster concerted multidisciplinary efforts needed to address societal grand challenges. In this commentary, we present an innovative model of cohort education, which equips graduate students with core skills and enables collaborative dissertation research among students. In addition, we provide an example of a program aimed at understanding the plant–soil microbiome, a critical research area that may yield significant advances in plant health and productivity.}, number={1}, journal={Agricultural & Environmental Letters}, publisher={Wiley}, author={Duckworth, Owen W. and Andrews, Megan Y. and Cubeta, Marc A. and Grunden, Amy M. and Ojiambo, Peter S.}, year={2017}, pages={170019} }
 @inproceedings{lin_dinh_sampath_akinci_2016, title={A Computational study of thin film dynamics on micro structured surfaces}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85002986155&partnerID=MN8TOARS}, DOI={10.1115/ht2016-7382}, abstractNote={The present study is motivated by interest in understanding of physical mechanisms that govern the effect of material and micro-structural characteristics of heat surface on boiling heat transfer and burnout at high heat fluxes. The effect was reported and investigated experimentally and analytically over several past decades. Only recently, with the advent of nanotechnology including microscale manufacturing, it becomes possible to perform high heat-flux boiling experiments with control of surface conditions.
               Of particular importance for practice is the potential for significant enhancement of boiling heat transfer (BHT) and critical heat flux (CHF) in pool and flow boiling on heaters with specially manufactured and controlled micro-structured surfaces. This enhancement is very important to a very wide range of engineering applications, like heat exchanger and cooling system, where maximum flux is needed. Currently, there are many controlled experiments that investigate such effect and they lend themselves a subject for detailed computational analysis.
               The focus of this study is micro-hydrodynamics of the evaporating thin liquid film at the receding triple contact line, corresponding to formation of dry spot in the footprint of a growing bubble. Parametric investigations are performed to assess the hypotheses that micro-structured surfaces enhance resilience to burnout due to residual liquid in the dry patch after contact line receding.
               Towards the study objective, a particle-based (mesh-less) method of computational fluid dynamics called Smoothed Particle Hydrodynamics (SPH) is adopted. The SPH method is selected for its capability to handle fluid dynamics in complex geometries and free surface problems without mass loss (characteristic of alternative interface capturing schemes used in mesh-based methods). Both surface tension and surface adhesion (hydrophilicity) are implemented and tested. The solid (heater) surface and manufactured micro-structures are represented by solid-type particles. Heat transfer, phase change (evaporation) and vapor dynamics are not included in the present simulation.
               The bouncing drop case measures the contact time of water droplet with solid surface. This case is used for “mesh” sensitivity (particle size) study and calibration of boundary conditions and surface tension coefficient.
               Subsequently, case studies are formulated and performed for contact line dynamics on heater surfaces with the fabricated Micro Pillar Arrays surfaces (MPA) and smooth surface. Variable characteristics include surface tension and pillar density on structured surface (modified by changing distance between pillars).
               First of all, residual fluid are found in all simulations with structured surface, while fluid are drained for smooth cases. For structured surface, it’s found that after the contact line recedes, fluid with higher surface tension resides in the dry patch more than fluid with lower coefficient, and the relation tends to be non-linear. While for smooth surface, all fluid will be drained after certain time and the relations are non-monotonic; it’s also found that the amount of residual fluid increase as the distance between pillars decreases until a limit. The fluid then starts to decrease with pillars being set further apart. The increase starts from 30 μm and the limit is around 10 μm.}, booktitle={Proceedings of the Asme Summer Heat Transfer Conference, 2016, vol 2}, author={Lin, L. Y. and Dinh, N. T. and Sampath, R. and Akinci, N.}, year={2016} }
 @article{burchhardt_miller_cline_cubeta_2017, title={Fine-Scale Genetic Structure and Reproductive Biology of the Blueberry Pathogen Monilinia vaccinii-corymbosi}, volume={107}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/PHYTO-02-16-0093-R}, DOI={10.1094/PHYTO-02-16-0093-R}, abstractNote={ The fungus Monilinia vaccinii-corymbosi, a pathogen of Vaccinium spp., requires asexual and sexual spore production to complete its life cycle. A recent study found population structuring of M. vaccinii-corymbosi over a broad spatial scale in the United States. In this study, we examined fine-scale genetic structuring, temporal dynamics, and reproductive biology within a 125-by-132-m blueberry plot from 2010 to 2012. In total, 395 isolates of M. vaccinii-corymbosi were sampled from infected shoots and fruit to examine their multilocus haplotype (MLH) using microsatellite markers. The MLH of 190 single-ascospore isolates from 21 apothecia was also determined. Little to no genetic differentiation and unrestricted gene flow were detected among four sampled time points and between infected tissue types. Discriminant analysis of principal components suggested genetic structuring within the field, with at least K = 3 genetically distinct clusters maintained over four sampled time points. Single-ascospore progeny from eight apothecia had identical MLH and at least two distinct MLH were detected from 13 apothecia. Tests for linkage disequilibrium suggested that genetically diverse ascospore progeny were the product of recombination. This study supports the idea that the fine-scale dynamics of M. vaccinii-corymbosi may be complex, with genetic structuring, inbreeding, and outcrossing detected in the study area. }, number={2}, journal={Phytopathology}, publisher={Scientific Societies}, author={Burchhardt, Kathleen M. and Miller, Megan E. and Cline, William O. and Cubeta, Marc A.}, year={2017}, month={Feb}, pages={231–239} }
 @article{pettersson_frampton_rönnberg_shew_benson_kohlway_escanferla_cubeta_2016, title={Increased diversity of Phytophthora species in Fraser fir Christmas tree plantations in the Southern Appalachians}, volume={32}, ISSN={0282-7581 1651-1891}, url={http://dx.doi.org/10.1080/02827581.2016.1265144}, DOI={10.1080/02827581.2016.1265144}, abstractNote={ABSTRACT Phytophthora root rot (PRR) disease afflicts significant economic losses to the Fraser fir Christmas tree industry. In previous surveys conducted in 1972 and from 1997 to 1998 in North Carolina, the incidence of PRR was ∼9.5% with Phytophthora cinnamomi identified as the predominant causal species isolated from infected roots of Fraser fir. Due to increased use of out-of-state planting stock since 2000, we suspected increased diversity of Phytophthora species. During 2014, we surveyed Fraser fir Christmas tree plantations in the Southern Appalachians of North Carolina, Tennessee and Virginia to determine the occurrence of pathogenic root-rotting species of Phytophthora. A weighted sampling strategy based on Christmas tree acreage was deployed to collect symptomatic Fraser fir roots from 103 commercial production fields in 14 counties. Six species of Phytophthora were isolated from infected roots sampled from 82 sites in 13 counties. Phytophthora cinnamomi, P. cryptogea and P. pini represented 70.3%, 23.1% and 1.1% of the 91 isolates. Phytophthora citrophthora, P. europaea and P. sansomeana accounted for the remaining 5.5% of the isolates and have not been identified in previously published Fraser fir surveys conducted in the region. The pathogenicity of P. citrophthora on Fraser fir was confirmed based on completion of Koch’s postulates.}, number={5}, journal={Scandinavian Journal of Forest Research}, publisher={Informa UK Limited}, author={Pettersson, M. and Frampton, J. and Rönnberg, J. and Shew, H. D. and Benson, D. M. and Kohlway, W. H. and Escanferla, M. E. and Cubeta, M. A.}, year={2016}, month={Dec}, pages={412–420} }
 @article{gonzalez_rodriguez-carres_boekhout_stalpers_kuramae_nakatani_vilgalys_cubeta_2016, title={Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales}, volume={120}, ISSN={["1878-6162"]}, DOI={10.1016/j.funbio.2016.01.012}, abstractNote={Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets were analysed individually and combined using Maximum Parsimony, Maximum Likelihood, and Bayesian Phylogenetic Inference methods. All analyses supported the monophyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. This analysis coupled with analyses of a larger sample of 165 rpb2 sequences of fungi in the Cantharellales supported a sister relationship between the Botryobasidiaceae and Ceratobasidiaceae and a sister relationship of the Tulasnellaceae with the rest of the Cantharellales. The inclusion of additional sequence data did not clarify incongruences observed in previous studies of Rhizoctonia fungi in the Cantharellales based on analyses of a single or multiple genes. The diversity of ecological and morphological characters associated with these fungi requires further investigation on character evolution for re-evaluating homologous and homoplasious characters.}, number={4}, journal={FUNGAL BIOLOGY}, author={Gonzalez, Dolores and Rodriguez-Carres, Marianela and Boekhout, Teun and Stalpers, Joost and Kuramae, Eiko E. and Nakatani, Andreia K. and Vilgalys, Rytas and Cubeta, Marc A.}, year={2016}, month={Apr}, pages={603–619} }
 @article{jiang_lee_cubeta_chen_2015, title={Characterization and colonization of endomycorrhizal Rhizoctonia fungi in the medicinal herb Anoectochilus formosanus (Orchidaceae)}, volume={25}, ISSN={0940-6360 1432-1890}, url={http://dx.doi.org/10.1007/s00572-014-0616-1}, DOI={10.1007/s00572-014-0616-1}, abstractNote={The medicinal effects and techniques for cultivating Anoectochilus formosanus are well-documented, but little is known about the mycorrhizal fungi associated with A. formosanus. Rhizoctonia (Thanatephorus) anastomosis group 6 (AG-6) was the most common species isolated from fungal pelotons in native A. formosanus and represented 67 % of the sample. Rhizoctonia (Ceratobasidium) AG-G, P, and R were also isolated and represent the first occurrence in the Orchidaceae. Isolates of AG-6, AG-R, and AG-P in clade I increased seed germination 44–91 % and promoted protocorm growth from phases III to VI compared to asymbiotic treatments and isolates of AG-G in clade II and Tulasnella species in clade III. All isolates in clades I to III formed fungal pelotons in tissue-cultured seedlings of A. formosanus, which exhibited significantly greater growth than nonmycorrhizal seedlings. An analysis of the relative effect of treatment ( $$ {\widehat{p}}_i $$ ) showed that the low level of colonization ( $$ {\widehat{p}}_i = 0.30\hbox{--} 0.47 $$ ) by isolates in clade I resulted in a significant increase in seedling growth compared to isolates in clades II (0.63–0.82) and III (0.63–0.75). There was also a negative correlation (r = −0.8801) with fresh plant weight and fungal colonization. Our results suggest that isolates in clade I may represent an important group associated with native populations of A. formosanus and can vary in their ability to establish a symbiotic association with A. formosanus. The results presented here are potentially useful for advancing research on the medicinal properties, production, and conservation of A. formosanus in diverse ecosystems.}, number={6}, journal={Mycorrhiza}, publisher={Springer Science and Business Media LLC}, author={Jiang, Jr-Hau and Lee, Yung-I and Cubeta, Marc A. and Chen, Lung-Chung}, year={2015}, month={Jan}, pages={431–445} }
 @article{miller_norris_cubeta_2015, title={Evaluation of boxwood cultivars for resistance to boxwood blight}, volume={10}, ISSN={2330-3123}, journal={Plant Disease Management Reports}, publisher={American Phytopathological Society}, author={Miller, M.E. and Norris, R. and Cubeta, M.A.}, year={2015}, pages={OT009} }
 @article{mothapo_chen_cubeta_grossman_fuller_shi_2015, title={Phylogenetic, taxonomic and functional diversity of fungal denitrifiers and associated N2O production efficacy}, volume={83}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2015.02.001}, DOI={10.1016/j.soilbio.2015.02.001}, abstractNote={Fungi generally dominate microbial biomass in various soils and play critical roles in ecosystem functioning including nutrient cycling, disease ecology and food production. Therefore, fungal denitrification, phenotypically typified by nitrous oxide (N2O) production, presents another avenue other than N mineralization and heterotrophic nitrification for progress to better understand the multiple roles of fungi in sustaining the biosphere. The discovery of N2O production and consequently denitrification in Fusarium oxysporum Schltdl. in early 1970's has led to identification of many taxonomically diverse species of N2O-producing fungi. This review evaluates the current status of knowledge on species composition of fungal denitrifiers and their N2O-producing activity. Here we describe challenges with assessment of fungal N2O-producing activity across genera and suggest prospects for future studies. We also discuss species diversity in order to gain knowledge of important taxonomic and phylogenetic groups mediating N2O production and provide insight on ecological cues associated with fungal N2O production. Currently, the extent to which species phylogeny and the functional trait, i.e. N2O-producing activity, are linked remains to be determined; even so, it is evident that some related taxa exhibit similar N2O production efficacy than distant relatives.}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Mothapo, Nape and Chen, Huaihai and Cubeta, Marc A. and Grossman, Julie M. and Fuller, Fred and Shi, Wei}, year={2015}, month={Apr}, pages={160–175} }
 @article{gkarmiri_finlay_alström_thomas_cubeta_högberg_2015, title={Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica}, volume={16}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-015-1758-z}, DOI={10.1186/s12864-015-1758-z}, abstractNote={Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Gkarmiri, Konstantia and Finlay, Roger D. and Alström, Sadhna and Thomas, Elizabeth and Cubeta, Marc A. and Högberg, Nils}, year={2015}, month={Aug} }
 @article{cubeta_thomas_dean_jabaji_neate_tavantzis_toda_vilgalys_bharathan_fedorova-abrams_et al._2014, title={Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP}, volume={2}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomeA.01072-14}, DOI={10.1128/genomeA.01072-14}, abstractNote={ABSTRACT
          
            The soil fungus
            Rhizoctonia solani
            is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence of
            R. solani
            strain Rhs1AP. A comprehensive understanding of the heterokaryotic genome complexity and organization of
            R. solani
            may provide insight into the plant disease ecology and adaptive behavior of the fungus.
          }, number={5}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Cubeta, M. A. and Thomas, E. and Dean, R. A. and Jabaji, S. and Neate, S. M. and Tavantzis, S. and Toda, T. and Vilgalys, R. and Bharathan, N. and Fedorova-Abrams, N. and et al.}, year={2014}, month={Oct} }
 @article{dorman_bazzle_cubeta_marks_2014, title={Feasibility of flotation concentration of fungal spores as a method to identify toxigenic mushrooms}, volume={12}, ISSN={2230-2034}, url={http://dx.doi.org/10.2147/vmrr.s67794}, DOI={10.2147/vmrr.s67794}, abstractNote={Purpose Mushroom poisoning is a recurring and challenging problem in veterinary medicine. Diagnosis of mushroom exposure in animals is hampered by the lack of rapid diagnostic tests. Our study evaluated the feasibility of using flotation concentration and microscopic evaluation of spores for mushroom identification. Evaluation of this method in living animals exposed to toxigenic mushrooms is limited by ethical constraints; therefore, we relied upon the use of an in vitro model that mimics the oral and gastric phases of digestion. Methods In our study, mycologist-identified toxigenic (poisonous) and nontoxigenic fresh mushrooms were collected in North Carolina, USA. In phase 1, quantitative spore recovery rates were determined following magnesium sulfate, modified Sheather’s sugar solution, and zinc sulfate flotation (n=16 fungal species). In phase 2, mushrooms (n=40 fungal species) were macerated and digested for up to 2 hours in a salivary and gastric juice simulant. The partially digested material was acid neutralized, filtered, and spores concentrated using zinc sulfate flotation followed by microscopic evaluation of spore morphology. Results Mean spore recovery rates for the three flotation fluids ranged from 32.5% to 41.0% (P=0.82). Mean (± standard error of the mean) Amanita spp. spore recovery rates were 38.1%±3.4%, 36.9%±8.6%, and 74.5%±1.6% (P=0.0012) for the magnesium sulfate, Sheather’s sugar, and zinc sulfate solutions, respectively. Zinc sulfate flotation following in vitro acid digestion (phase 2) yielded spore numbers adequate for microscopic visualization in 97.5% of trials. The most common spore shapes observed were globose, spiked, elliptical, smooth and reticulate. Conclusion Flotation can concentrate mushroom spores; however, false negative results can occur. Spore morphology could not be used to differentiate species of mushroom-forming fungi since the spore shape and surface characteristics seen in the present study were often observed with multiple species of mushroom-forming fungi.}, journal={Veterinary Medicine: Research and Reports}, publisher={Informa UK Limited}, author={Dorman, David and Bazzle, Lisa and Cubeta, Marc and Marks, Steven}, year={2014}, month={Dec}, pages={1} }
 @article{losada_pakala_fedorova_joardar_shabalina_hostetler_pakala_zafar_thomas_rodriguez-carres_et al._2014, title={Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3}, volume={352}, ISSN={["1574-6968"]}, DOI={10.1111/1574-6968.12387}, abstractNote={The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Losada, Liliana and Pakala, Suman B. and Fedorova, Natalie D. and Joardar, Vinita and Shabalina, Svetlana A. and Hostetler, Jessica and Pakala, Suchitra M. and Zafar, Nikhat and Thomas, Elizabeth and Rodriguez-Carres, Marianela and et al.}, year={2014}, month={Mar}, pages={165–173} }
 @article{burchhardt_cubeta_2015, title={Population Structure of the Blueberry Pathogen Monilinia vaccinii-corymbosi in the United States}, volume={105}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-03-14-0074-r}, abstractNote={ The fungus Monilinia vaccinii-corymbosi causes disease of blueberry (Vaccinium section Cyanococcus) shoots, flowers, and fruit. The objective of our research was to examine the population biology and genetics of M. vaccinii-corymbosi in the United States. A total of 480 samples of M. vaccinii-corymbosi were collected from 18 blueberry fields in 10 states; one field in Georgia, Massachusetts, Maine, Michigan, Mississippi, New Jersey, New York, Oregon, and Washington and nine fields in North Carolina. Analysis with 10 microsatellite markers revealed 247 unique multilocus haplotypes (MLHs), with 244 MLHs detected within 11 fields in the Northeast, Northwest, Midwest, and Southeast and three MLHs detected within seven fields in the Southeast United States. Genetic similarity and low genetic diversity of M. vaccinii-corymbosi isolates from the seven fields in the Southeast United States suggested the presence of an expansive, self-fertile population. Tests for linkage disequilibrium within 10 fields that contained ≥12 MLHs supported random mating in six fields and possible inbreeding and/or self-fertilization in four fields. Analysis of molecular variance, discriminate analysis of principal components, and Bayesian cluster analysis provided evidence for population structure and restricted gene flow among fields. This research represents the first comprehensive investigation of the genetic diversity and structure of field populations of M. vaccinii-corymbosi. }, number={4}, journal={PHYTOPATHOLOGY}, author={Burchhardt, Kathleen M. and Cubeta, Marc A.}, year={2015}, month={Apr}, pages={533–541} }
 @article{chamoun_samsatly_pakala_cubeta_jabaji_2015, title={Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection}, volume={290}, ISSN={["1617-4623"]}, DOI={10.1007/s00438-014-0962-x}, abstractNote={Rhizoctonia solani is a plant pathogenic fungus that causes black scurf on tubers and stem and stolon canker on underground parts of potato plant. Early in the season, the fungus attacks germinating sprouts underground before they emerge from the soil. Damage at this stage results in delayed emergence of weakened plants with poor and uneven stands. The mechanism underlying this phenomenon has been investigated in this study by coupling a cDNA-suppression subtractive hybridization (SSH) library to differential screening to identify transcripts of R. solani that are down-regulated during infection of potato sprouts. We report on the identification of 33 unique genes with functions related to carbohydrate binding, vitamin synthesis, pathogenicity, translation, ATP and nucleic acid binding and other categories. RACE-PCR was used to clone and characterize the first full-length cDNA clones, RSENDO1 and RSGLYC1 that encode for an eukaryotic delta-endotoxin CytB protein and an intracellular glycosyl hydrolase, respectively. Quantitative real-time PCR revealed the down-regulation of RSENDO1 during infection of potato sprouts and the up-regulation of RSGLYC1 when the fungus was grown on a cellulose-based nutrient medium. In contrast, additional experiments have highlighted the down-regulation of RSENDO1 when R. solani was co-cultured with the mycoparasite Stachybotrys elegans and the bacterial antagonist Bacillus subtilis B26. These results advance our understanding of R. solani-potato interaction in subterranean parts of the plant. Such approaches could be considered in building an efficient integrated potato disease management program.}, number={3}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Chamoun, Rony and Samsatly, Jamil and Pakala, Suman B. and Cubeta, Marc A. and Jabaji, Suha}, year={2015}, month={Jun}, pages={877–900} }
 @article{mccormick_cubeta_grand_2013, title={Geography and hosts of the wood decay fungi <em>Fomes fasciatus</em> and <em>Fomes fomentarius</em> in the United States}, volume={8}, ISSN={1937-786X}, url={http://dx.doi.org/10.2509/naf2013.008.002}, DOI={10.2509/naf2013.008.002}, abstractNote={Comprehensive United States county distribution maps of Fomes fasciatus and F. fomentarius were developed based on peer-reviewed publications, records from mycological herbaria and collections made for this study. The geographic distribution was expanded for both species to include a total of seven counties in five states not included in previous publications and records. North Carolina and Tennessee were the only states where both species occurred, but their distributions did not overlap when resolved to the county level. Both fungi occurred on a diverse range of hardwood tree hosts, and in this study, 11 and 17 new hosts associations were identified for F. fasciatus and F. fomentarius , respectively. The extension of host distributions beyond the known range for each fungus suggests that other delimiting factors may contribute to the distribution of F. fasciatus and F. fomentarius .}, number={0}, journal={North American Fungi}, publisher={Pacific Northwest Fungi Project}, author={McCormick, Meghan A. and Cubeta, Marc A. and Grand, Larry F.}, year={2013}, month={Jan}, pages={1} }
 @article{bartz_glassbrook_danehower_cubeta_2013, title={Modulation of the phenylacetic acid metabolic complex by quinic acid alters the disease-causing activity of Rhizoctonia solani on tomato}, volume={89}, ISSN={0031-9422}, url={http://dx.doi.org/10.1016/j.phytochem.2012.09.018}, DOI={10.1016/j.phytochem.2012.09.018}, abstractNote={The metabolic control of plant growth regulator production by the plant pathogenic fungus Rhizoctonia solani Kühn (teleomorph = Thanatephorus cucumeris (A.B. Frank) Donk) and consequences associated with the parasitic and saprobic activity of the fungus were investigated. Fourteen genetically distinct isolates of the fungus belonging to anastomosis groups (AG) AG-3, AG-4, and AG-1-IA were grown on Vogel's minimal medium N with and without the addition of a 25 mM quinic acid (QA) source of carbon. The effect of QA on fungal biomass was determined by measuring the dry wt of mycelia produced under each growth condition. QA stimulated growth of 13 of 14 isolates of R. solani examined. The production of phenylacetic acid (PAA) and the chemically related derivatives 2-hydroxy-PAA, 3-hydroxy-PAA, 4-hydroxy-PAA, and 3-methoxy-PAA on the two different media was compared by gas chromatography coupled with mass spectrometry (GC–MS). The presence of QA in the growth medium of R. solani altered the PAA production profile, limiting the conversion of PAA to derivative forms. The effect of QA on the ability of R. solani to cause disease was examined by inoculating tomato (Solanum lycopersicum L.) plants with 11 isolates of R. solani AG-3 grown on media with and without the addition of 25 mM QA. Mean percent survival of tomato plants inoculated with R. solani was significantly higher when the fungal inoculum was generated on growth medium containing QA. The results of this study support the hypotheses that utilization of QA by R. solani leads to reduced production of the plant growth regulators belonging to the PAA metabolic complex which can suppress plant disease development.}, journal={Phytochemistry}, publisher={Elsevier BV}, author={Bartz, Faith E. and Glassbrook, Norman J. and Danehower, David A. and Cubeta, Marc A.}, year={2013}, month={May}, pages={47–52} }
 @article{mothapo_chen_cubeta_shi_2013, title={Nitrous oxide producing activity of diverse fungi from distinct agroecosystems}, volume={66}, ISSN={["1879-3428"]}, DOI={10.1016/j.soilbio.2013.07.004}, abstractNote={Fungi represent a significant component of the soil microbial community and play critical ecological roles in carbon and nitrogen mediated processes. Therefore, fungi capable of nitrous oxide (N2O) production may have great implications to soil N2O emission. The primary objective of this research was to identify and characterize N2O-producing fungi in agricultural soil systems and determine their relative physiological responses to inorganic N, pH and oxygen availability. Soil samples were collected from five agricultural-based systems: conventional farming, organic farming, integrated crop and livestock, plantation forestry, and an abandoned agriculture field subjected to natural succession. Fungi were isolated from soil and examined for N2O production in a nitrate-containing liquid Czapek medium amended with or without cycloheximide or streptomycin. Fungal population levels were similar among the five systems, ranging from 1.1 to 3.7 × 105 colony-forming units per gram of soil. One hundred-fifty one fungal colonies were selected based on colony morphology and tested for N2O production. About half (i.e., 45%) of tested isolates representing at least 16 genera and 30 species of filamentous fungi were capable of producing N2O. Neocosmospora vasinfecta exhibited the highest production of N2O in laboratory based assays, followed by Aspergillus versicolor, A. oryzae, A. terreus, Fusarium oxysporum and Penicillium pinophilum. Ten selected N2O-producing fungus isolates were subsequently evaluated to determine the influence of nitrogen species, pH and O2 on N2O production. Seven of the 10 selected isolates had 65% or greater N2O production in a nitrite than a nitrate medium. Ninety and 60%, of isolates showed greatest N2O production at neutral pH 7.0 and ≤5% headspace O2 conditions, respectively. Our results demonstrate that N2O-producing fungi were prevalent in the five soil systems and production of N2O varied among isolates examined under different imposed abiotic conditions in the laboratory.}, journal={SOIL BIOLOGY & BIOCHEMISTRY}, author={Mothapo, Nape V. and Chen, Huaihai and Cubeta, Marc A. and Shi, Wei}, year={2013}, month={Nov}, pages={94–101} }
 @article{mccormick_grand_post_cubeta_2013, title={Phylogenetic and phenotypic characterization of Fomes fasciatus and Fomes fomentarius in the United States}, volume={105}, ISSN={["1557-2536"]}, DOI={10.3852/12-336}, abstractNote={The wood-decay fungi Fomes fasciatus and F. fomentarius share many morphological characters that historically have made species delimitation challenging. We examined morphological, molecular and physiological characters of basidiomata and pure cultures of F. fasciatus and F. fomentarius sampled from multiple plant hosts and geographic regions in the United States to determine whether they support separation of the two species. We find that mean basidiospore size is significantly larger in F. fomentarius and represents the most informative morphological character for delineating the species. Basidiomata and pore-surface shape provided additional resolution of the species, but these characters often overlap and are more variable than basidiospore size. Phylogenetic analyses of ITS and RPB2 sequences suggest that F. fasciatus and F. fomentarius represent distinct evolutionary lineages. The two species share less than 88% maximum identity for the ITS region. Limited intraspecific sequence variation at each locus also was observed. In vitro experiments of hyphal-growth response to a wide range of temperatures support differences in physiology between the two species.}, number={6}, journal={MYCOLOGIA}, author={McCormick, Meghan A. and Grand, Larry F. and Post, Justin B. and Cubeta, Marc A.}, year={2013}, pages={1524–1534} }
 @article{skamnaki_peumans_kantsadi_cubeta_plas_pakala_zographos_smagghe_nierman_van damme_et al._2013, title={Structural analysis of the Rhizoctoniasolani agglutinin reveals a domain-swapping dimeric assembly}, volume={280}, ISSN={["1742-4658"]}, DOI={10.1111/febs.12190}, abstractNote={Rhizoctonia solani agglutinin (RSA) is a 15.5‐kDa lectin accumulated in the mycelium and sclerotia of the soil born plant pathogenic fungus R. solani. Although it is considered to serve as a storage protein and is implicated in fungal insecticidal activity, its physiological role remains unclear as a result of a lack of any structure/function relationship information. Glycan arrays showed that RSA displays high selectivity towards terminal nonreducing N‐acetylgalactosamine residues. We determined the amino acid sequence of RSA and also determined the crystal structures of the free form and the RSA–N‐acetylgalactosamine complex at 1.6 and 2.2 Å resolution, respectively. RSA is a homodimer comprised of two monomers adopting the β‐trefoil fold. Each monomer accommodates two different carbohydrate‐binding sites in an asymmetric way. Despite RSA topology similarities with R‐type lectins, the two‐monomer assembly involves an N‐terminal swap, thus creating a dimer association novel to R‐type lectins. Structural characterization of the two carbohydrate‐binding sites offers insights on the structural determinants of the RSA carbohydrate specificity.DatabaseStructural data have been deposited in the Protein Data Bank database under accession numbers 4G9M and 4G9N.Structured digital abstractRSA and RSA bind by x-ray crystallography (View interaction)}, number={8}, journal={FEBS JOURNAL}, author={Skamnaki, Vassiliki T. and Peumans, Willy J. and Kantsadi, Anastassia L. and Cubeta, Marc A. and Plas, Kirsten and Pakala, Suman and Zographos, Spyridon E. and Smagghe, Guy and Nierman, William C. and Van Damme, Els J. M. and et al.}, year={2013}, month={Apr}, pages={1750–1763} }
 @article{ferrucho_ceresini_ramirez-escobar_mcdonald_cubeta_garcia-dominguez_2013, title={The Population Genetic Structure of Rhizoctonia solani AG-3PT from Potato in the Colombian Andes}, volume={103}, ISSN={["0031-949X"]}, DOI={10.1094/phyto-11-12-0278-r}, abstractNote={The soilborne fungus Rhizoctonia solani anastomosis group 3 (AG-3PT) is a globally important potato pathogen. However, little is known about the population genetic processes affecting field populations of R. solani AG-3PT, especially in the South American Colombian Andes, which is near the center of diversity of the two most common groups of cultivated potato, Solanum tuberosum and S. phureja. We analyzed the genetic structure of 15 populations of R. solani AG-3PT infecting potato in Colombia using 11 simple-sequence repeat (SSR) markers. In total, 288 different multilocus genotypes were identified among 349 fungal isolates. Clonal fractions within field populations were 7 to 33%. RSTstatistics indicated a very low level of population differentiation overall, consistent with high contemporary gene flow, though moderate differentiation was found for the most distant southern populations. Genotype flow was also detected, with the most common genotype found widely distributed among field populations. All populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction, but two populations displayed evidence of inbreeding.}, number={8}, journal={PHYTOPATHOLOGY}, author={Ferrucho, Rosa L. and Ceresini, Paulo C. and Ramirez-Escobar, Ursula M. and McDonald, Bruce A. and Cubeta, Marc A. and Garcia-Dominguez, Celsa}, year={2013}, month={Aug}, pages={862–869} }
 @article{toda_strausbaugh_rodriguez-carres_cubeta_2012, title={Characterization of a Basidiomycete fungus from stored sugar beet roots}, volume={104}, ISSN={["0027-5514"]}, DOI={10.3852/10-416}, abstractNote={Eighteen isolates from sugar beet roots associated with an unknown etiology were characterized based on observations of morphological characters, hyphal growth at 4–28 C, production of phenol oxidases and sequence analysis of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA (rDNA). The isolates did not produce asexual or sexual spores, had binucleate hyphal cells with clamp connections, grew 4–22 C with estimated optimal growth at 14.5 C and formed a dark brown pigment on potato dextrose or malt extract agar amended with 0.5% tannic acid. Color changes observed when solutions of gum guiac, guiacol and syringaldzine were applied directly to mycelium grown on these media indicated that all isolates produced phenol oxidases. Sequences of ITS and LSU regions on the rDNA gene from 15 isolates were 99.2–100% identical, and analysis of sequence data with maximum likelihood and maximum parsimony suggest that the isolates from sugar beet roots are phylogenetically related to Athelia bombacina, Granulobasidium vellereum and Cyphella digitalis. High statistical support for both loci under different criteria confirmed that Athelia bombacina was consistently the closest known relative to the sugar beet isolates. Additional taxonomic investigations are needed before species can be clarified and designated for these isolates.}, number={1}, journal={MYCOLOGIA}, author={Toda, Takeshi and Strausbaugh, Carl A. and Rodriguez-Carres, Marianela and Cubeta, Marc A.}, year={2012}, pages={70–78} }
 @article{bartz_glassbrook_danehower_cubeta_2012, title={Elucidating the role of the phenylacetic acid metabolic complex in the pathogenic activity of Rhizoctonia solani anastomosis group 3}, volume={104}, ISSN={["0027-5514"]}, DOI={10.3852/11-084}, abstractNote={The soil fungus Rhizoctonia solani produces phytotoxic phenylacetic acid (PAA) and hydroxy (OH-) and methoxy (MeO-) derivatives of PAA. However, limited information is available on the specific role that these compounds play in the development of Rhizoctonia disease symptoms and concentration(s) required to induce a host response. Reports that PAA inhibits the growth of R. solani conflict with the established ability of the fungus to produce and metabolize PAA. Experiments were conducted to clarify the role of the PAA metabolic complex in Rhizoctonia disease. In this study the concentration of PAA and derivatives required to induce tomato root necrosis and stem canker, in the absence of the fungus, and the concentration that inhibits mycelial growth of R. solani were determined. The effect of exogenous PAA and derivatives of PAA on tomato seedling growth also was investigated. Growth of tomato seedlings in medium containing 0.1–7.5 mM PAA and derivatives induced necrosis of up to 85% of root system. Canker development resulted from injection of tomato seedling stems with 7.5 mM PAA, 3-OH-PAA, or 3-MeO-PAA. PAA in the growth medium reduced R. solani biomass, with 50% reduction observed at 7.5 mM. PAA, and derivatives were quantified from the culture medium of 14 isolates of R. solani belonging to three distinct anastomosis groups by GC-MS. The quantities ranged from below the limit of detection to 678 nM, below the concentrations experimentally determined to be phytotoxic. Correlation analyses revealed that isolates of R. solani that produced high PAA and derivatives in vitro also caused high mortality on tomato seedlings. The results of this investigation add to the body of evidence that the PAA metabolic complex is involved in Rhizoctonia disease development but do not indicate that production of these compounds is the primary or the only determinant of pathogenicity.}, number={4}, journal={MYCOLOGIA}, author={Bartz, Faith E. and Glassbrook, Norman J. and Danehower, David A. and Cubeta, Marc A.}, year={2012}, pages={793–803} }
 @article{burchhardt_cubeta_2012, title={Microsatellite marker development for the plant pathogenic fungus Monilinia vaccinii-corymbosi}, volume={12}, number={5}, journal={Molecular Ecology Resources}, author={Burchhardt, K. and Cubeta, M.A.}, year={2012}, pages={972–974} }
 @article{abello_ai_altmann_bernardi_bonato_burchhardt_chen_chen_cizkova_clouet_et al._2012, title={Permanent genetic resources added to molecular ecology resources database 1 April 2012-31 May 2012}, volume={12}, number={5}, journal={Molecular Ecology Resources}, author={Abello, P. and Ai, W. M. and Altmann, C. and Bernardi, G. and Bonato, O. and Burchhardt, K. M. and Chen, X. and Chen, Z. J. and Cizkova, D. and Clouet, C. and et al.}, year={2012}, pages={972–974} }
 @article{thomas_pakala_fedorova_nierman_cubeta_2012, title={Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani}, volume={158}, ISSN={["1873-4863"]}, DOI={10.1016/j.jbiotec.2012.01.024}, abstractNote={The aneuploid and heterokaryotic nuclear condition of the soil fungus Rhizoctonia solani have provided challenges in obtaining a complete genome sequence. To better aid in the assembly and annotation process, a protoplast and single nucleotide polymorphism (SNP)-based method was developed to identify regenerated protoplasts with a reduced nuclear genome. Protocol optimization experiments showed that enzymatic digestion of mycelium from a 24 h culture of R. solani increased the proportion of protoplasts with a diameter of ≤7.5 μm and 1–4 nuclei. To determine whether strains regenerated from protoplasts with a reduced number of nuclei were genetically different from the parental strain, triallelic SNPs identified from variance records of the genomic DNA sequence reads of R. solani were used in PCR-based genotyping assays. Results from 16 of the 24 SNP-based PCR assays provided evidence that one of the three alleles was missing in the 11 regenerated protoplast strains, suggesting that these strains represent a reduced genomic complement of the parental strain. The protoplast and triallelic SNP-based method used in this study may be useful in strain development and analysis of other basidiomycete fungi with complex nuclear genomes.}, number={3}, journal={JOURNAL OF BIOTECHNOLOGY}, author={Thomas, Elizabeth and Pakala, Suman and Fedorova, Natalie D. and Nierman, William C. and Cubeta, Marc A.}, year={2012}, month={Apr}, pages={144–150} }
 @article{aliferis_cubeta_jabaji_2011, title={Chemotaxonomy of fungi in the Rhizoctonia solani species complex performing GC/MS metabolite profiling}, volume={9}, ISSN={1573-3882 1573-3890}, url={http://dx.doi.org/10.1007/s11306-011-0340-1}, DOI={10.1007/s11306-011-0340-1}, number={S1}, journal={Metabolomics}, publisher={Springer Science and Business Media LLC}, author={Aliferis, Konstantinos A. and Cubeta, Marc A. and Jabaji, Suha}, year={2011}, month={Jul}, pages={159–169} }
 @article{yin_kone_rodriguez-carres_cubeta_burpee_fonsah_csinos_ji_2011, title={First Report of Root Rot Caused by Binucleate Rhizoctonia Anastomosis Group F on Musa spp}, volume={95}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-08-10-0602}, abstractNote={ A research program was initiated at the University of Georgia in 2003 to identify banana cultivars suitable for production in the coastal and southern areas of the state. During a root disease survey conducted in October 2007 on bananas (Musa spp.) grown at the University of Georgia Bamboo Farm and Coastal Gardens in Savannah, GA, root lesions and root rot were observed on banana cvs. Gold Finger, Kandarian, and Manzano. Root lesions were dark brown to black and irregular in shape, with partial or entire roots affected. Lateral roots and outer layers of cord roots (roots arising from interior layers of the corm) of infected plants were blackened and rotted. Diseased root samples were collected from three plants of each cultivar, surface sterilized with 0.6% sodium hypochlorite, and placed on tannic acid benomyl agar (TABA). Pure cultures of the fungus consistently associated with diseased tissue were obtained by subculturing hyphal tips on TABA. Mycelia of the fungus on potato dextrose agar (PDA) were light to deep brown and the hyphae tended to branch at right angles. A septum was present in each hyphal branch near the point of origin and a slight constriction at the branch was observed. The hyphae of two isolates were stained with 0.6% phenosafranin and 3% KOH and binucleate hyphal cells were observed. On the basis of these morphological features, the isolates appeared to be binucleate Rhizoctonia anamorphs (teleomorph Ceratobasidium Rogers). For molecular identification, the internal transcribed spacer (ITS) regions and the 5.8S gene from rDNA of the isolates were cloned and sequenced (GenBank Accession No. HQ168370). The ITS regions (775 bp) were 100% identical between the two isolates and 99% identical to Ceratobasidium sp. AG-F strain SIR-1 isolated from sweet potato in Japan (GenBank Accession No. AF354085). The anastomosis group of the isolates was confirmed by pairing with strain SIR-1 on PDA. On the basis of morphological and molecular characteristics and the anastomosis assay, the two isolates were identified as a Ceratobasidium sp. AG-F (1–3). Pathogenicity assays were conducted by inoculating banana plants (cv. Golden pillow, synonym = Manzano) grown in pots under greenhouse conditions (25 to 27°C). Twenty wheat seeds infested with each isolate were placed uniformly around each plant at a depth of 10 cm in the soil. The plants were incubated in the greenhouse and the roots were examined 2 months after inoculation. Brown-to-black lesions and root rot, identical to symptoms associated with field banana roots, were observed on all inoculated plants but not on the noninoculated control plants. The fungus was reisolated from affected root samples and the identity was confirmed by morphological and molecular characteristics and the anastomosis assay. To our knowledge, this is the first report of banana root rot caused by binucleate Rhizoctonia anastomosis group F. With the increased interest in producing bananas for food and ornamental purposes, the occurrence of Ceratobasidium root rot on bananas needs to be considered when designing disease management programs and searching for suitable cultivars for banana production.  References: (1) L. L. Burpee et al. Mycologia 70:1281, 1978. (2) D. González et al. Mycologia 93:1138, 2001. (3) B. Sneh et al. Identification of Rhizoctonia Species. The American Phytopathological Society, St. Paul, MN. 1991. }, number={4}, journal={PLANT DISEASE}, author={Yin, J. and Kone, D. and Rodriguez-Carres, M. and Cubeta, M. A. and Burpee, L. L. and Fonsah, E. G. and Csinos, A. S. and Ji, P.}, year={2011}, month={Apr}, pages={490–490} }
 @article{woodhall_webb_harper_peters_rodriguez-carres_cubeta_2011, title={First report of a new binucleate Rhizoctonia on potato tubers in the UK}, volume={23}, ISSN={2044-0588}, url={http://dx.doi.org/10.5197/j.2044-0588.2011.023.031}, DOI={10.5197/j.2044-0588.2011.023.031}, abstractNote={A sample of potato tubers of cv. Navan displaying growth cracking (up to 10 mm in depth and width) and elephant hide symptoms often associated with Rhizoctonia potato disease were received by Fera for diagnosis. The tubers, originating from a commercial farm in Cornwall UK, were harvested in October 2009. For each symptom, pure Rhizoctonia cultures were obtained as previously described (Woodhall et al., 2007) and DNA was extracted from the resulting cultures and tested for R. solani anastomosis groups (AGs) 2-1, 3, 5, and 8 using real-time PCR (Budge et al., 2009). AG-3 was consistently found from tuber areas showing severe elephant hide, sunken areas and growth cracking symptoms. However, isolates consistently recovered from areas of less severe elephant hide symptoms, which often covered as much as 50% of the tuber surface (Fig. 1), could not be assigned to a specific AG by this method. To determine the identity of these isolates, the hyphae of one representative isolate was stained with trypan blue in lactoglycerol (0.1% stain made with 67ml lactoglycerol, 33ml distilled water and 0.1g trypan blue) to visualise nuclei. Under 400x magnification, each cell had two nuclei indicating the strain was a binucleate Rhizoctonia species (BNR). The mean width of 20 mature hyphae was 5.1 μm (range 3.81 to 7.63 μm, s.d.= 0.89 μm) and consistent with BNR species. Since previous studies have demonstrated the utility of DNA-based assays to identify AG in the absence of tester isolates for typing, sequencing of the rDNA ITS region was undertaken for the isolate with primers ITS1 and ITS4 (White et al., 1990). The resulting sequence (GenBank Accession No. FR828480) was compared to other sequences in GenBank. No near identical matches were found suggesting the isolate could be a unique strain of a particular BNR or belong to a previously undescribed AG. The isolate was therefore deposited into the Fera culture collection as Accession No. cc43. To determine whether the isolate was the causal agent of the observed symptoms the following experimental protocol was carried out. Potato minitubers (cv. Santé) were placed at 100 mm depth in 2 litre pots with John Innes Number 3 compost. Three 10 mm PDA plugs from a 14-day-old culture of the isolate were placed on top of each minituber. Pots were held in a controlled environment room at 18°C with 50% relative humidity and watered as required. After four weeks, plants were removed and assessed for disease. Small lesions (<5 mm) were present on roots and stems (Fig. 2). Infected lenticels and similar mild elephant hide symptom were present on the seed tuber. BNR was consistently isolated from symptomatic tissue. Here, we report the finding of a previously undescribed strain of BNR occurring in a UK potato crop. This is the first account of an infection of potato caused by Rhizoctonia other than R. solani in the UK. R. solani has been associated with Rhizoctonia potato disease in UK potatoes, with a number of different isolates assigned to AGs 2-1, 3 and 5 (Chand & Logan, 1983; Woodhall et al., 2007). We further demonstrate the ability of this isolate to cause disease on potato roots and stems. Future work on Rhizoctonia potato disease in the UK should also consider examining the relative contribution of BNR to the epidemiology of Rhizoctonia diseases of potato. The authors thank support from the AHDB Potato Council, UK.}, journal={New Disease Reports}, publisher={British Society for Plant Pathology}, author={Woodhall, J.W. and Webb, K.M. and Harper, G. and Peters, J.C. and Rodriguez-Carres, M. and Cubeta, M.A.}, year={2011}, month={Jun}, pages={31} }
 @article{copes_rodriguez-carres_toda_rinehart_cubeta_2011, title={Seasonal Prevalence of Species of Binucleate Rhizoctonia Fungi in Growing Medium, Leaf Litter, and Stems of Container-Grown Azalea}, volume={95}, ISSN={["0191-2917"]}, DOI={10.1094/pdis-11-10-0796}, abstractNote={ Rhizoctonia web blight is an annual problem on container-grown azalea (Rhododendron spp.) in the southern and eastern United States but little is documented about the distribution or persistence of Rhizoctonia spp. in container-grown azalea. Sixty web-blight-damaged azalea plants (‘Gumpo White’) were collected in August 2005 and 2006 and arranged in a completely randomized design on an outdoor irrigation pad. A nylon mesh bag containing 30 necrotic leaves collected from web-blight-damaged ‘Gumpo White’ azalea plants were placed on the surface of the medium under the plant canopy in each container to simulate leaf litter. Ten plants were destructively sampled into eight zones by dividing stems into three zones (lengths of 0 to 2, 4 to 6, and 9 to 15 cm above the medium surface), bagged leaves into one leaf litter zone, and the medium into four zones (three horizontal layers: 1 to 3, 3 to 7, and 7 to 10 cm below the medium surface, with the middle layer further divided by removing the central 7.5-cm-diameter core) in December, February, and May. Only the three stem zones were sampled from 10 plants in early and late June and late July. Of 8,940 total isolations, 3,655 fungi with morphological characteristics of a Rhizoctonia sp. were recovered. Percent recovery differed from the eight zones (P < 0.0001) but did not differ between years (P = 0.3950) and sampling times (P = 0.1896). Frequency of recovery of Rhizoctonia spp. was highest from the lower stem and the leaf litter, and decreased with distance from the leaf litter. Recovery from stems over the six sample times was analyzed separately. Percent recovery differed between stem zones (P < 0.0001), sample times (P = 0.0478), and experiment years (P < 0.0001). In both years, mean recovery of Rhizoctonia spp. was higher from the lower stem and decreased with distance to the upper stem layer. From a subsample of 145 isolates, 95.1% were identified as binucleate Rhizoctonia (BNR) anastomosis groups (AGs)-A, -G, -K, -R, -S, and -U (-P), and 2.8 and 2.1% were Rhizoctonia solani AG-2 and an uncultured Laetisaria sp., respectively. Based on frequency analysis, recovery of BNR AGs differed by plant zone (P < 0.0001) but not over sample times (P = 0.4831). The six AGs of BNR are the predominant Rhizoctonia fungi occupying the habitat niches in container-grown azalea, with little change in population frequency and composition from fall to summer; thus, BNR pathogenic and nonpathogenic to azalea have established a mixed Rhizoctonia community on container-grown azalea. }, number={6}, journal={PLANT DISEASE}, author={Copes, Warren E. and Rodriguez-Carres, Marianela and Toda, Takeshi and Rinehart, Tim A. and Cubeta, Marc A.}, year={2011}, month={Jun}, pages={705–711} }
 @misc{samuels_ismaiel_rosmana_junaid_guest_mcmahon_keane_purwantara_lambert_rodriguez-carres_et al._2012, title={Vascular Streak Dieback of cacao in Southeast Asia and Melanesia: in planta detection of the pathogen and a new taxonomy}, volume={116}, ISSN={["1878-6162"]}, DOI={10.1016/j.funbio.2011.07.009}, abstractNote={Vascular Streak Dieback (VSD) disease of cacao (Theobroma cacao) in Southeast Asia and Melanesia is caused by a basidiomycete (Ceratobasidiales) fungus Oncobasidium theobromae (syn. =Thanatephorus theobromae). The most characteristic symptoms of the disease are green-spotted leaf chlorosis or, commonly since about 2004, necrotic blotches, followed by senescence of leaves beginning on the second or third flush behind the shoot apex, and blackening of infected xylem in the vascular traces at the leaf scars resulting from the abscission of infected leaves. Eventually the shoot apex is killed and infected branches die. In susceptible cacao the fungus may grow through the xylem down into the main stem and kill a mature cacao tree. Infections in the stem of young plants prior to the formation of the first 3-4 lateral branches usually kill the plant. Basidiospores released from corticioid basidiomata developed on leaf scars or along cracks in the main vein of infected leaves infect young leaves. The pathogen commonly infects cacao but there are rare reports from avocado. As both crops are introduced to the region, the pathogen is suspected to occur asymptomatically in native vegetation. The pathogen is readily isolated but cultures cannot be maintained. In this study, DNA was extracted from pure cultures of O. theobromae obtained from infected cacao plants sampled from Indonesia. The internal transcribed spacer region (ITS), consisting of ITS1, 5.8S ribosomal RNA and ITS2, and a portion of nuclear large subunit (LSU) were sequenced. Phylogenetic analysis of ITS sequences placed O. theobromae sister to Ceratobasidium anastomosis groups AG-A, AG-Bo, and AG-K with high posterior probability. Therefore the new combination Ceratobasidium theobromae is proposed. A PCR-based protocol was developed to detect and identify C. theobromae in plant tissue of cacao enabling early detection of the pathogen in plants. A second species of Ceratobasidium, Ceratobasidium ramicola, identified through ITS sequence analysis, was isolated from VSD-affected cacao plants in Java, and is widespread in diseased cacao collected from Indonesia.}, number={1}, journal={FUNGAL BIOLOGY}, author={Samuels, Gary J. and Ismaiel, Adnan and Rosmana, Ade and Junaid, Muhammad and Guest, David and Mcmahon, Peter and Keane, Philip and Purwantara, Agus and Lambert, Smilja and Rodriguez-Carres, Marianela and et al.}, year={2012}, month={Jan}, pages={11–23} }
 @article{sullivan_parks_cubeta_gallup_melton_moyer_shew_2010, title={An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure}, volume={94}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-94-4-0455}, abstractNote={ One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field. }, number={4}, journal={PLANT DISEASE}, author={Sullivan, M. J. and Parks, E. J. and Cubeta, M. A. and Gallup, C. A. and Melton, T. A. and Moyer, J. W. and Shew, H. D.}, year={2010}, month={Apr}, pages={455–460} }
 @article{kaye_moyer_parks_carbone_cubeta_2011, title={Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia}, volume={101}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-01-10-0035}, abstractNote={ Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. In this study, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of Tomato spotted wilt virus (TSWV) from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of 1 or 2 predominant haplotypes and >100 haplotypes represented by a single isolate. No specific haplotypes were associated with geographic area, peanut cultivar, or year of isolation. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for positive selection on single amino acids in each gene on a background of predominant purifying selection acting upon each locus. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Estimates of the population mutation rate suggest that mutation has had a significant effect on the shaping of this population and, together with purifying selection, these forces have been the predominant evolutionary forces influencing the TSWV population in peanut in North Carolina and Virginia. }, number={1}, journal={PHYTOPATHOLOGY}, author={Kaye, A. C. and Moyer, J. W. and Parks, E. J. and Carbone, I. and Cubeta, M. A.}, year={2011}, month={Jan}, pages={147–153} }
 @article{ferrucho_zala_zhang_cubeta_garcia-dominguez_ceresini_2009, title={Highly polymorphic in silico-derived microsatellite loci in the potato-infecting fungal pathogen Rhizoctonia solani anastomosis group 3 from the Colombian Andes}, volume={9}, ISSN={["1755-0998"]}, DOI={10.1111/j.1755-0998.2009.02553.x}, abstractNote={AbstractFourteen polymorphic microsatellite DNA markers derived from the draft genome sequence of Rhizoctonia solani anastomosis group 3 (AG‐3), strain Rhs 1AP, were designed and characterized from the potato‐infecting soil fungus R. solani AG‐3. All loci were polymorphic in two field populations collected from Solanum tuberosum and S. phureja in the Colombian Andes. The total number of alleles per locus ranged from two to seven, while gene diversity (expected heterozygosity) varied from 0.11 to 0.81. Considering the variable levels of genetic diversity observed, these markers should be useful for population genetic analyses of this important dikaryotic fungal pathogen on a global scale.}, number={3}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Ferrucho, R. L. and Zala, M. and Zhang, Z. and Cubeta, M. A. and Garcia-Dominguez, C. and Ceresini, P. C.}, year={2009}, month={May}, pages={1013–1016} }
 @article{kanetis_wang_wadl_neufeld_holmes_ojiambo_cubeta_trigiano_2009, title={Microsatellite loci in the downy mildew pathogen, Pseudoperonospora cubensis}, volume={9}, number={6}, journal={Molecular Ecology Resources}, author={Kanetis, L. and Wang, X. and Wadl, P.A. and Neufeld, K. and Holmes, G.A. and Ojiambo, P. and Cubeta, M.A. and Trigiano, R.T.}, year={2009}, pages={1460–1466} }
 @article{almany_de arruda_arthofer_atallah_beissinger_berumen_bogdanowicz_brown_bruford_burdine_et al._2009, title={Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009}, volume={9}, ISSN={["1755-098X"]}, url={http://europepmc.org/abstract/med/21564933}, DOI={10.1111/j.1755-0998.2009.02759.x}, abstractNote={AbstractThis article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross‐tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo‐atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross‐tested in both species.}, number={6}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Almany, Glenn R. and De Arruda, Mauricio P. and Arthofer, Wolfgang and Atallah, Z. K. and Beissinger, Steven R. and Berumen, Michael L. and Bogdanowicz, S. M. and Brown, S. D. and Bruford, Michael W. and Burdine, C. and et al.}, year={2009}, month={Nov}, pages={1460–1466} }
 @inbook{ivors_f.e._cubeta_2009, place={St. Paul, Minnesota}, edition={2}, title={Rhizoctonia foliar blight of tomato}, booktitle={Compendium of Tomato Diseases}, publisher={APS Press}, author={Ivors, K. and F.E., Bartz and Cubeta, M.A.}, editor={Miller, S. and Jones, J.Editors}, year={2009} }
 @inbook{charlton_tavantzis_cubeta_2008, title={Detection of Double-Stranded RNA Elements in the Plant Pathogenic Fungus Rhizoctonia solani}, ISBN={9781588297990 9781597450621}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-59745-062-1_14}, DOI={10.1007/978-1-59745-062-1_14}, abstractNote={Many species of fungi have been shown to harbor double-stranded RNA (dsRNA) elements. A single fungal isolate of Rhizoctonia solani may have as many as five different dsRNA elements within them. The presence of specific dsRNA elements influence pathogenicity in host plants.}, booktitle={Plant Pathology}, publisher={Humana Press}, author={Charlton, Nikki D. and Tavantzis, Stellos M. and Cubeta, Marc A.}, year={2008}, month={Nov}, pages={171–182} }
 @article{charlton_carbone_tavantzis_cubeta_2008, title={Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi}, volume={100}, ISSN={["0027-5514"]}, DOI={10.3852/07-108R}, abstractNote={Isolates from closely related fungi in the Rhizoctonia species complex were examined for the occurrence of the M2 double-stranded RNA (dsRNA) by amplifying a conserved 1000 nucleotide region of the dsRNA with reverse transcription PCR. The M2 dsRNA was detected in representative isolates belonging to three anastomosis groups (AG) of R. solani (AG-1-IA, AG-4 and AG-6; teleomorph = Thanatephorus) and four AGs of binucleate Rhizoctonia (AGA, AG-F, AG-R and AG-U; teleomorph = Ceratobasidium). Amplified PCR products from the 3′ region of the M2 dsRNA from a representative sample of 12 isolates from eight different AGs were sequenced and subjected to parsimony analysis and coalescent simulations to infer ancestral lineages and to reconstruct the ancestral history of haplotypes. Seven dsRNA haplotypes were inferred from the sample of 12 isolates. One haplotype was composed of only isolates of Ceratobasidium belonging to different AGs. The rooted gene genealogies from coalescent simulations suggested that the ancestral M2 dsRNA haplotype most likely evolved in Thanatephorus (anamorph = R. solani AG-1-IA) and has been acquired recently by isolates of Ceratobasidium. Reconstruction of the ancestral history of haplotypes with a parsimony-based approach that assumes both mutation and recombination suggested that four haplotypes recombined before coalescing to their most recent common ancestor, while three haplotypes coalesced without recombination in the recent past. There was no unique association of haplotype within a specific AG of either Ceratobasidium or Thanatephorus to support co-evolution of the M2 dsRNA within the fungal host. To our knowledge this is the first report of a dsRNA occurring in Ceratobasidium that also is present in Thanatephorus.}, number={4}, journal={MYCOLOGIA}, author={Charlton, Nikki D. and Carbone, Ignazio and Tavantzis, Stellos M. and Cubeta, Marc A.}, year={2008}, pages={555–564} }
 @article{rinehart_copes_toda_cubeta_2007, title={Genetic characterization of binucleate Rhizoctonia species causing web blight on azalea in Mississippi and Alabama}, volume={91}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-91-5-0616}, abstractNote={ Web blight on containerized azalea is an annual problem for commercial nurseries during summer months in the southern United States. Losses to web blight are associated with the cost of fungicide applications, delayed marketing of diseased plants, and plant death. Two hundred and eleven isolates of binucleate Rhizoctonia were recovered from azalea leaves with web blight symptoms from two nurseries in Mississippi and Alabama over 3 years. The internal transcribed spacer region (ITS) of the ribosomal DNA (rDNA) was sequenced from all isolates to determine genetic identity. A single anastomosis group (AG) of binucleate Rhizoctonia represented 92% of the samples collected from infected leaves. Genetic data and hyphal fusion experiments confirmed that these isolates belong to AG-U, which was recently identified from root and stem infections on miniature rose in Japan. Isolates of binucleate Rhizoctonia belonging to anastomosis groups AG-R, CAG-7 (=AG-S), and AG-G were also identified in the sample in low frequency. This is the first report of the occurrence of binucleate Rhizoctonia AG-U in the United States. }, number={5}, journal={PLANT DISEASE}, author={Rinehart, T. A. and Copes, W. E. and Toda, T. and Cubeta, M. A.}, year={2007}, month={May}, pages={616–623} }
 @inbook{cubeta_porter_mozley-standridge_2007, place={Boca Raton, FL}, edition={2nd}, title={Laboratory exercises with zoosporic plant pathogens}, ISBN={9781420046700 9781482226935}, booktitle={Plant Pathology: Concepts and Laboratory Exercises}, publisher={CRC Press}, author={Cubeta, M. and Porter, D. and Mozley-Standridge, S.}, editor={Trigiano, R.N. and Windham, M.T.Editors}, year={2007} }
 @article{ceresini_shew_james_vilgalys_cubeta_2007, title={Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci}, volume={7}, ISSN={1471-2148}, url={http://dx.doi.org/10.1186/1471-2148-7-163}, DOI={10.1186/1471-2148-7-163}, abstractNote={The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89).Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi ST = 0.257, significant at P < 0.05) but not for locus pP42F (Phi ST = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3.The two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.}, number={1}, journal={BMC Evolutionary Biology}, publisher={Springer Science and Business Media LLC}, author={Ceresini, Paulo C and Shew, H David and James, Timothy Y and Vilgalys, Rytas J and Cubeta, Marc A}, year={2007}, pages={163} }
 @inbook{mozley-standridge_porter_cubeta_2007, place={Boca Raton, FL}, edition={2nd}, title={Slimes Molds and Zoosporic Fungi}, ISBN={9781420046700 9781482226935}, booktitle={Plant Pathology: Concepts and Laboratory Exercises}, publisher={CRC Press}, author={Mozley-Standridge, S. and Porter, D. and Cubeta, M.}, editor={Trigiano, R.N. and Windham, M.T.Editors}, year={2007} }
 @article{charlton_cubeta_2007, title={Transmission of the M2 double-stranded RNA in Rhizoctonia solani anastomosis group 3 (AG-3)}, volume={99}, ISSN={["1557-2536"]}, DOI={10.3852/mycologia.99.6.859}, abstractNote={Horizontal transmission of the 3.57 kb M2 double-stranded RNA (dsRNA) between mycelia of somatically incompatible isolates of Rhizoctonia solani anastomosis group 3 (AG-3), an economically important pathogen of cultivated plants in the family Solanaceae, was investigated. Nine donor isolates of R. solani AG-3 containing the M2 dsRNA were paired on potato-dextrose agar with each of three different recipient isolates where the M2 dsRNA was absent. Reverse-transcription PCR (RT-PCR) was used to detect horizontal transmission of the M2 dsRNA via hyphal anastomosis from donor to recipient isolates by examining hyphal explants taken 3 cm from the hyphal interaction zone. PCR-RFLP genetic-based markers of two nuclear loci and one mitochondrial locus were used to confirm identity and transmission between donor and recipient isolates of R. solani AG-3. The frequency of transmission observed between 72 pairings of the eight donor and three recipient isolates was approximately 4% of the total pairings, and differences in the phenotype of the recipient isolates after acquisition of the M2 dsRNA via horizontal transmission were observed. To our knowledge this represents the first demonstration of transmission of dsRNA between genetically different individuals of R. solani confirmed with nuclear and mitochondrial markers. These results suggest that transmission can occur between somatically incompatible isolates of R. solani AG-3 but that maintenance of the dsRNA in the recipient isolates was not stable after repeated subculturing on nutrient medium.}, number={6}, journal={MYCOLOGIA}, author={Charlton, Nikki D. and Cubeta, Marc A.}, year={2007}, pages={859–867} }
 @article{charlton_cubeta_2007, title={Transmission of the M2 double-stranded RNA in Rhizoctonia solani anastomosis group 3 (AG-3)}, volume={99}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/15572536.2007.11832517}, DOI={10.1080/15572536.2007.11832517}, abstractNote={Horizontal transmission of the 3.57 kb M2 double-stranded RNA (dsRNA) between mycelia of somatically incompatible isolates of Rhizoctonia solani anastomosis group 3 (AG-3), an economically important pathogen of cultivated plants in the family Solanaceae, was investigated. Nine donor isolates of R. solani AG-3 containing the M2 dsRNA were paired on potato-dextrose agar with each of three different recipient isolates where the M2 dsRNA was absent. Reverse-transcription PCR (RT-PCR) was used to detect horizontal transmission of the M2 dsRNA via hyphal anastomosis from donor to recipient isolates by examining hyphal explants taken 3 cm from the hyphal interaction zone. PCR-RFLP genetic-based markers of two nuclear loci and one mitochondrial locus were used to confirm identity and transmission between donor and recipient isolates of R. solani AG-3. The frequency of transmission observed between 72 pairings of the eight donor and three recipient isolates was approximately 4% of the total pairings, and differences in the phenotype of the recipient isolates after acquisition of the M2 dsRNA via horizontal transmission were observed. To our knowledge this represents the first demonstration of transmission of dsRNA between genetically different individuals of R. solani confirmed with nuclear and mitochondrial markers. These results suggest that transmission can occur between somatically incompatible isolates of R. solani AG-3 but that maintenance of the dsRNA in the recipient isolates was not stable after repeated subculturing on nutrient medium.}, number={6}, journal={Mycologia}, publisher={Informa UK Limited}, author={Charlton, Nikki D. and Cubeta, Marc A.}, year={2007}, month={Nov}, pages={859–867} }
 @inbook{keinath_cubeta_langston_2006, place={New York, NY}, title={Cabbage Diseases, Ecology and Control}, booktitle={Encyclopedia of Pest Management}, publisher={Taylor & Francis}, author={Keinath, A.P. and Cubeta, M.A. and Langston, D.B., Jr}, editor={Pimentel, DavidEditor}, year={2006} }
 @article{gonzalez_cubeta_vilgalys_2006, title={Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex}, volume={40}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2006.03.022}, abstractNote={The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and β-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph = Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph = Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.}, number={2}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Gonzalez, Dolores and Cubeta, Marc A. and Vilgalys, Rytas}, year={2006}, month={Aug}, pages={459–470} }
 @inbook{payne_cubeta_2005, title={Biology and Detection of Fungal Pathogens of Humans and Plants}, ISBN={9780120884834}, url={http://dx.doi.org/10.1016/b978-012088483-4/50009-3}, DOI={10.1016/b978-012088483-4/50009-3}, abstractNote={This chapter reviews fungi, their taxonomy, growth, reproduction, pathogenicity, epidemiology, detection, and identification. Fungi have greatly shaped the history of humankind. However, not all fungi are beneficial; some fungi are harmful pathogens and can cause diseases. They represent an important group of pathogens that significantly impact human and plant health and are responsible for the majority of plant diseases and important agents of infectious diseases of immuno compromised humans. Kingdom Fungi include four phyla: Ascomycota (sac fungi), Basidiomycota (club and mushroom fungi; rusts; and smuts), Chytridiomycota (chytrids), and Zygomycota (bread molds), and are often referred to as the "true fungi" or Eumycota. Disease is the result of an interaction between a pathogen and a susceptible host within a favorable environment. Repeated dispersal and cycles of infection on the same plant are common attributes of many plant pathogens. In contrast, fungal diseases of humans are usually not communicable. Polymerase Chain Reaction (PCR) and Deoxyribonucleic Acid (DNA) sequence based methods allow a closer examination of the ecology and epidemiology of human and plant pathogens. Although databases are useful in identifying a wide range of fungi, in certain instances, these available databases may not be sufficient to place a DNA sequence within a previously sampled genus or species. A powerful tool for the identification of fungi is the detection of DNA sequence that varies from multiple regions of the fungal genome coupled with appropriate statistical analysis of the data. As newer techniques —such as; PCR, micro fluidic methods, mitochondrial, and nuclear DNA sequence data are available, rapid identification of genetically distinct individuals will be possible, facilitating fungal forensics.}, booktitle={Microbial Forensics}, publisher={Elsevier}, author={Payne, Gary A. and Cubeta, Marc A.}, year={2005}, pages={109–130} }
 @article{abad_moyer_kennedy_holmes_cubeta_2005, title={Tomato spotted wilt virus on potato in eastern North Carolina}, volume={82}, ISSN={["1874-9380"]}, DOI={10.1007/BF02853592}, number={3}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, author={Abad, JA and Moyer, JW and Kennedy, GG and Holmes, GA and Cubeta, MA}, year={2005}, pages={255–261} }
 @article{bush_carson_cubeta_hagler_payne_2004, title={Infection and fumonisin production by Fusarium verticillioides in developing maize kernels}, volume={94}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.2004.94.1.88}, abstractNote={ Fusarium ear rot and fumonisin contamination are serious problems for maize growers, particularly in the southeastern United States. The lack of maize genotypes highly resistant to infection by Fusarium verticillioides or to fumonisin contamination emphasizes the need for management strategies to prevent contamination by this mycotoxin. Information on the initial appearance of infection and fumonisin contamination of kernels and their increase over time is needed to determine if early harvest may be an appropriate control strategy. Maize ears from replicated studies at two locations in eastern North Carolina were harvested weekly, starting 2 weeks after pollination and continuing for 14 weeks. The percentage of kernels infected with F. verticillioides and the fumonisin contamination in the harvested samples were determined. Kernel infection by F. verticillioides and fumonisin contamination appeared as kernels neared physiological maturity and increased up to the average harvest date for maize in North Carolina. Beyond this date, the concentrations of fumonisin fluctuated. Under years conducive for fumonisin contamination, early harvest (greater than 25% grain moisture) may help reduce the level of contamination. }, number={1}, journal={PHYTOPATHOLOGY}, author={Bush, BJ and Carson, ML and Cubeta, MA and Hagler, WM and Payne, GA}, year={2004}, month={Jan}, pages={88–93} }
 @article{ceresini_shew_vilgalys_gale_cubeta_2003, title={Detecting migrants in populations of Rhizoctonia solani anastomosis group 3 from potato in North Carolina using multilocus genotype probabilities}, volume={93}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO.2003.93.5.610}, abstractNote={ The relative contribution of migration of Rhizoctonia solani anastomosis group 3 (AG-3) on infested potato seed tubers originating from production areas in Canada, Maine, and Wisconsin (source population) to the genetic diversity and structure of populations of R. solani AG-3 in North Carolina (NC) soil (recipient population) was examined. The frequency of alleles detected by multilocus polymerase chain reaction-restriction fragment length polymorphisms, heterozygosity at individual loci, and gametic phase disequilibrium between all pairs of loci were determined for subpopulations of R. solani AG-3 from eight sources of potato seed tubers and from five soils in NC. Analysis of molecular variation revealed little variation between seed source and NC recipient soil populations or between subpopulations within each region. Analysis of population data with a Bayesian-based statistical method previously developed for detecting migration in human populations suggested that six multilocus genotypes from the NC soil population had a statistically significant probability of being migrants from the northern source population. The one-way (unidirectional) migration of genotypes of R. solani AG-3 into NC on infested potato seed tubers from Canada, Maine, and Wisconsin provides a plausible explanation for the lack of genetic subdivision (differentiation) between populations of the pathogen in NC soils or between the northern source and the NC recipient soil populations. }, number={5}, journal={PHYTOPATHOLOGY}, author={Ceresini, PC and Shew, HD and Vilgalys, RJ and Gale, LR and Cubeta, MA}, year={2003}, month={May}, pages={610–615} }
 @inbook{cubeta_porter_mozley_2003, title={Laboratory Exercises with Zoosporic Plant Pathogens}, ISBN={0849310377 020350657X}, booktitle={Plant Pathology: Concepts and Laboratory Exercises}, author={Cubeta, M.A. and Porter, D. and Mozley, S.E.}, editor={Trigiano, R.N. and Windham, M.T. and Windham, A.S.Editors}, year={2003}, pages={173–192} }
 @inbook{mozley_porter_cubeta_2003, place={Boca Raton, FL}, title={Slime Molds and Zoosporic Fungi}, ISBN={9780429211287}, url={http://dx.doi.org/10.1201/b12388-21}, DOI={10.1201/b12388-21}, booktitle={Plant Pathology: Concepts and Laboratory Exercises}, publisher={CRC Press}, author={Mozley, S. and Porter, D. and Cubeta, M.}, editor={Trigiano, R.N. and Windham, M.T. and Windham, A.S.Editors}, year={2003}, month={Jul}, pages={179–191} }
 @article{hollowell_shew_cubeta_wilcut_2003, title={Weed species as hosts of Sclerotinia minor in peanut fields}, volume={87}, ISSN={["0191-2917"]}, DOI={10.1094/PDIS.2003.87.2.197}, abstractNote={ Bleached stems and sclerotia were observed on winter annual weed species growing in harvested peanut fields in northeastern North Carolina in March 2001. Each field had a history of Sclerotinia blight caused by Sclerotinia minor. Symptomatic plants were collected and brought back to the laboratory for identification and isolation. S. minor was isolated and Koch's postulates were fulfilled to confirm pathogenicity of S. minor on nine weed species. They included Lamium aplexicaule (henbit), Cardamine parviflora (smallflowered bittercress), Stellaria media (common chickweed), Cerastium vulgatum (mouse-ear chickweed), Coronopus didymus (swinecress), Oenothera laciniata (cutleaf eveningprimrose), Conyza canadensis (horseweed), Brassica kaber (wild mustard), and Arabidopsis thaliana (mouse-ear cress). This is the first report of these species as hosts of S. minor in the natural environment. All isolates of S. minor obtained from the weed species were pathogenic to peanut. }, number={2}, journal={PLANT DISEASE}, author={Hollowell, JE and Shew, BB and Cubeta, MA and Wilcut, JW}, year={2003}, month={Feb}, pages={197–199} }
 @article{ceresini_shew_vilgalys_cubeta_2002, title={Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina}, volume={94}, ISSN={["0027-5514"]}, DOI={10.2307/3761778}, abstractNote={Anastomosis group 3 (AG-3) of Rhizoctonia solani (teleomorph = Thanatephorus cucumeris) is frequently associated with diseases of potato (AG-3 PT) and tobacco (AG-3 TB). Although isolates of R. solani AG-3 from these two Solanaceous hosts are somatically related based on anastomosis reaction and taxonomically related based on fatty acid, isozyme and DNA characters, considerable differences are evident in their biology, ecology, and epidemiology. However, genetic diversity among field populations of R. solani AG-3 PT and TB has not been documented. In this study, the genetic diversity of field populations of R. solani AG-3 PT and AG-3 TB in North Carolina was examined using somatic compatibility and amplified fragment length polymorphism (AFLP) criteria. A sample of 32 isolates from potato and 36 isolates from tobacco were paired in all possible combinations on PDA plus activated charcoal and examined for their resulting somatic interactions. Twenty-eight and eight distinct somatic compatibility groups (SCG) were identified in the AG-3 PT and AG-3 TB samples, respectively. AFLP analyses indicated that each of the 32 AG-3 PT isolates had a distinct AFLP phenotype, whereas 28 AFLP phenotypes were found among the 36 isolates of AG-3 TB. None of the AG-3 PT isolates were somatically compatible or shared a common AFLP phenotype with any AG-3 TB isolate. Clones (i.e., cases where two or more isolates were somatically compatible and shared the same AFLP phenotype) were identified only in the AG-3 TB population. Four clones from tobacco represented 22% of the total population. All eight SCG from tobacco were associated with more than one AFLP phenotype. Compatible somatic interactions between AG-3 PT isolates occurred only between certain isolates from the same field (two isolates in each of four different fields), and when this occurred AFLP phenotypes were similar but not identical.}, number={3}, journal={MYCOLOGIA}, author={Ceresini, PC and Shew, HD and Vilgalys, RJ and Cubeta, MA}, year={2002}, pages={437–449} }
 @article{ceresini_shew_vilgalys_rosewich_cubeta_2002, title={Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina}, volume={94}, ISSN={["0027-5514"]}, DOI={10.2307/3761779}, abstractNote={A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify and differentiate genotypes of Rhizoctonia solani anastomosis group 3 subgroup PT (AG-3 PT), a fungal pathogen of potato. Polymorphic co-dominant single-locus PCR-RFLP markers were identified after sequencing of clones from a genomic library and digestion with restriction enzymes. Multilocus genotypes were determined by a combination of PCR product and digestion with a specific restriction enzyme for each of seven loci. A sample of 104 isolates from one commercial field in each of five counties in eastern North Carolina was analyzed, and evidence for high levels of gene flow between populations was revealed. When data were clone-corrected and samples pooled into one single North Carolina population, random associations of alleles were found for all loci or pairs of loci, indicating random mating. However, when all genotypes were analyzed, the observed genotypic diversity deviated from panmixia and alleles within and between loci were not randomly associated. These findings support a model of population structure for R. solani AG-3 PT on potato that includes both recombination and clonality.}, number={3}, journal={MYCOLOGIA}, author={Ceresini, PC and Shew, HD and Vilgalys, RJ and Rosewich, UL and Cubeta, MA}, year={2002}, pages={450–460} }
 @article{wangsomboondee_groves_shoemaker_cubeta_ristaino_2002, title={Phytophthora infestans populations from tomato and potato in North Carolina differ in genetic diversity and structure}, volume={92}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.2002.92.11.1189}, abstractNote={ Phytophthora infestans causes a destructive disease on tomato and potato. In North Carolina (NC) potatoes are mostly grown in the east, whereas tomatoes are grown in the mountainous areas in the western part of the state. Five genotypes of P. infestans were identified from 93 and 157 isolates collected from tomato and potato over a 5 year period between 1993 and 1998. All isolates collected from potato in eastern NC were the US-8 genotype, whereas only a single isolate was the US-1 genotype. Tuber blight was found on immature daughter tubers in a single field in 1997, however infection on mature tubers was not observed. Within potato fields, a range of sensitivity to metalaxyl was observed among isolates but all were either intermediate or highly resistant to the fungicide. In contrast, isolates from tomatoes included previously reported US-7 and US-8 genotypes and two new genotypes called US-18 and US-19 (A2 mating type, allozyme genotype Gpi 100/100 and Pep 92/100). These genotypes had unique restriction fragment length polymorphism banding patterns, were sensitive to metalaxyl, and have not been reported elsewhere. All genotypes, with the exception of the US-1, were the Ia mitochondrial haplotype. Thus, isolates of P. infestans from tomato were more genetically diverse over time in NC than those from potato and include two new genotypes that are sensitive to metalaxyl. }, number={11}, journal={PHYTOPATHOLOGY}, author={Wangsomboondee, T and Groves, CT and Shoemaker, PB and Cubeta, MA and Ristaino, JB}, year={2002}, month={Nov}, pages={1189–1195} }
 @article{gonzalez_carling_kuninaga_vilgalys_cubeta_2001, title={Ribosomal DNA systematics of Ceratobasidium and Thanatephorus with Rhizoctonia anamorphs}, volume={93}, ISSN={["0027-5514"]}, DOI={10.2307/3761674}, abstractNote={The phylogenetic relationships of anastomosis groups (AG) of Rhizoctonia associated with Ceratobasidium and Thanatephorus teleomorphs were determined by cladistic analyses of internal transcribed spacer (ITS) and 28S large subunit (LSU) regions of nuclear-encoded ribosomal DNA (rDNA). Combined analyses of ITS and LSU rDNA sequences from 41 isolates representing 28 AG of Ceratobasidium and Thanatephorus supported at least 12 monophyletic groupings within Ceratobasidium and Thanatephorus. There was strong support for separation of Ceratobasidium and Thanatephorus, however, six sequences representing different AG of Ceratobasidium grouped with certain sequences within the Thanatephorus clade. Phylogenetic analysis of ITS sequence data from 122 isolates revealed 31 genetically distinct groups from Thanatephorus (21 groups) and Ceratobasidium (10 groups) that corresponded well with previously recognized AG or AG subgroups. Although phylogenetic analysis of ITS sequences provided evidence that several AG of Ceratobasidium may be more closely related with some AG from Thanatephorus, these relationships were not as strongly supported by bootstrap analysis.}, number={6}, journal={MYCOLOGIA}, author={Gonzalez, D and Carling, DE and Kuninaga, S and Vilgalys, R and Cubeta, MA}, year={2001}, pages={1138–1150} }
 @article{elliott_jardin_batson_caceres_brannen_howell_benson_conway_rothrock_schneider_et al._2001, title={Viability and stability of biological control agents on cotton and snap bean seeds}, volume={57}, ISSN={1526-498X 1526-4998}, url={http://dx.doi.org/10.1002/ps.342}, DOI={10.1002/ps.342}, abstractNote={AbstractCotton and snap bean were selected for a multi‐year, multi‐state regional (south‐eastern USA) research project to evaluate the efficacy of both commercial and experimental bacterial and fungal biological control agents for the management of damping‐off diseases. The goal for this portion of the project was to determine the viability and stability of biological agents after application to seed. The biological seed treatments used included: (1) Bacillaceae bacteria, (2) non‐Bacillaceae bacteria, (3) the fungus Trichoderma and (4) the fungus Beauveria bassiana. Seed assays were conducted to evaluate the following application factors: short‐term (≤3 months) stability after seed treatment; quality (ie isolate purity); compatibility with chemical pesticides and other biocontrol agents; application uniformity between years and plant species. For the bacterial treatments, the Bacillaceae genera (Bacillus and Paenibacillus) maintained the greatest population of bacteria per seed, the best viability over time and the best application uniformity across years and seed type. The non‐Bacillaceae genera Burkholderia and Pseudomonas had the least viability and uniformity. Although Beauveria bassiana was only evaluated one year, the seed fungal populations were high and uniform. The seed fungal populations and uniformity for the Trichoderma isolates were more variable, except for the commercial product T‐22. However, this product was contaminated with a Streptomyces isolate in both the years that it was evaluated. The study demonstrated that Bacillaceae can be mixed with Trichoderma isolates or with numerous pesticides to provide an integrated pest control/growth enhancement package.© 2001 Society of Chemical Industry}, number={8}, journal={Pest Management Science}, publisher={Wiley}, author={Elliott, Monica L and Jardin, Elizabeth A Des and Batson, William E and Caceres, Jacobo and Brannen, Philip M and Howell, Charles R and Benson, D Michael and Conway, Kenneth E and Rothrock, Craig S and Schneider, Raymond W and et al.}, year={2001}, pages={695–706} }
 @article{keinath_batson_caceres_elliott_sumner_brannen_rothrock_huber_benson_conway_et al._2000, title={Evaluation of biological and chemical seed treatments to improve stand of snap bean across the southern United States}, volume={19}, ISSN={["1873-6904"]}, DOI={10.1016/S0261-2194(00)00047-8}, abstractNote={Thirteen bacterial, four fungal, and four chemical fungicide seed treatments were evaluated one or more years in multiple field locations across the southern United States. Snap bean seed was treated in bulk with fungicides and most biocontrol agents, shipped to individual locations, and stored until planting or treated on site immediately before planting. Populations of biocontrol agents on seeds were assayed after seed treatment and planting. Analysis of variance of percent plant stand at 28 days after sowing revealed highly significant (P<0.01) effects of location and treatment in 1996, 1997 and 1998. A treatment by location interaction also occurred in 1996 and 1997. When treatments tested in two or three years were analyzed together, no biological seed treatments significantly affected percent stand. Carboxin significantly increased percent stand compared with nontreated seed in data sets combined from 1997 and 1998 and 1996 to 1998; captan and carboxin plus metalaxyl also increased stand in 1997 and 1998. Improvements in efficacy and consistency of biological seed treatments are necessary before they can be recommended for use in snap bean production.}, number={7}, journal={CROP PROTECTION}, author={Keinath, AP and Batson, WE and Caceres, J and Elliott, ML and Sumner, DR and Brannen, PM and Rothrock, CS and Huber, DM and Benson, DM and Conway, KE and et al.}, year={2000}, month={Aug}, pages={501–509} }
 @article{hudyncia_shew_cody_cubeta_2000, title={Evaluation of wounds as a factor to infection of cabbage by ascospores of Sclerotinia sclerotiorum}, volume={84}, ISSN={["0191-2917"]}, DOI={10.1094/PDIS.2000.84.3.316}, abstractNote={ A semi-selective medium was used to examine the aerobiology of ascospores of Sclerotinia sclerotiorum in five commercial cabbage fields in eastern North Carolina. Ascospores were present in all five fields from 26 September to 30 November. However, numbers of ascospores varied greatly depending on location, sampling date, and time. In general, peak ascospore deposition occurred between 11:00 A.M. and 1:00 P.M., with the number of colonies recovered ranging from 3 to 55/dish (9 cm in diameter). Peak ascospore numbers at all locations were found from mid- to late October, but a second, smaller peak was also evident at each location in late November. Information obtained was employed to evaluate the role of wounding in infection of cabbage by ascospores of S. sclerotiorum in controlled environmental chambers. A method for production and release of ascospores of S. sclerotiorum was employed in controlled-environment chambers for the inoculation of cabbage plants with one of three representative foliar wounds: a bruise, a cut, or a non-lethal freeze. Wounding treatments were applied to 7-week-old cabbage plants, misting was added to maintain continuous leaf wetness, and ascospores were released from apothecia twice daily for four consecutive days. Spore trapping with a semi-selective medium indicated that inoculum was evenly distributed within the chambers and deposition was similar to levels recorded in the field. At 31 days after inoculation, disease incidence ranged from 0% on the control to 96% on the freeze treatments. Freeze-treated plants showed the highest disease severity throughout the entire incubation period. Mean area under the disease progress curve of severity values were 0, 0.2, 34 and 60 for the control, cut, bruise, and freeze treatments, respectively. Results indicate that freeze and bruise injuries are important factors associated with infection of cabbage by S. sclerotiorum. }, number={3}, journal={PLANT DISEASE}, author={Hudyncia, J and Shew, HD and Cody, BR and Cubeta, MA}, year={2000}, month={Mar}, pages={316–320} }
 @article{crozier_creamer_cubeta_2000, title={Fertilizer management impacts on stand establishment, disease, and yield of Irish potato}, volume={43}, ISSN={["1871-4528"]}, DOI={10.1007/BF02358513}, number={1}, journal={POTATO RESEARCH}, author={Crozier, CR and Creamer, NG and Cubeta, MA}, year={2000}, pages={49–59} }
 @article{cubeta_cody_sugg_crozier_2000, title={Influence of soil calcium, potassium, and pH on development of leaf tipburn of cabbage in eastern North Carolina}, volume={31}, ISSN={["1532-2416"]}, DOI={10.1080/00103620009370435}, abstractNote={Abstract Three hypotheses that involved manipulation of soil calcium (Ca), potassium (K), and pH in relation to the occurrence of leaf tipburn of cabbage in eastern North Carolina (NC) were formulated and tested: 1) adding K to soil will increase (induce) leaf tipburn; 2) adding Ca and K together to soil will block K‐related tipburn induction, and 3) raising soil pH to levels of 6.0 to 6.5 will decrease leaf tipburn. Six experiments were conducted in commercial cabbage production fields in eastern NC in 1996 and 1997 to test these hypotheses. Hypothesis 1 was accepted since higher rates of K significantly (p<0.05) increased leaf K concentration, soil K content and leaf tipburn incidence compared with the control. Total cabbage yield increased as K rates increased, however, significant differences were only observed between the control and the highest rate (365 kg K ha‐1) in 1996. Hypothesis 2 was accepted since adding increased amounts of Ca and K. did not significantly increase leaf tipburn incidence. Hypothesis 3 was rejected since a range of soil pH from 5.3 to 6.6 did not increase or decrease leaf tipburn incidence, nutrient uptake or total yield. These data suggest that leaf tipburn of cabbage can be increased (induced) with excessive K fertilization and that this practice may be associated with the disorder observed in NC. Also, the addition of Ca with K may potentially reduce the risk associated with K‐related leaf tipburn of cabbage.}, number={3-4}, journal={COMMUNICATIONS IN SOIL SCIENCE AND PLANT ANALYSIS}, author={Cubeta, MA and Cody, BR and Sugg, RE and Crozier, CR}, year={2000}, pages={259–275} }
 @inbook{cubeta_vilgalys_2000, title={Rhizoctonia}, volume={4}, booktitle={Encyclopedia of microbiology  (2nd ed.)}, publisher={San Diego, Calif.: Academic Press}, author={Cubeta, M. A. and Vilgalys, R.}, year={2000}, pages={109–116} }
 @article{creamer_crozier_cubeta_1999, title={Influence of seedpiece spacing and population on yield, internal quality, and economic performance of Atlantic, Superior, and Snowden potato varieties in eastern North Carolina}, volume={76}, ISSN={["0003-0589"]}, DOI={10.1007/BF02853623}, number={5}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, author={Creamer, NG and Crozier, CR and Cubeta, MA}, year={1999}, pages={257–261} }
 @article{ross_keinath_cubeta_1998, title={Biological control of wirestem on cabbage using binucleate Rhizoctonia spp.}, volume={17}, ISSN={["1873-6904"]}, DOI={10.1016/S0261-2194(97)00109-9}, abstractNote={Binucleate Rhizoctonia (BNR) was investigated for biological control of wirestem on cabbage, caused by Rhizoctonia solani anastomosis group (AG) 4. Cabbage seedlings colonized with BNR isolate B901 (AG-G), 232-CG (AG-G), or PDS26E (AG unknown) were transplanted into infested field plots. In the fall of 1994 and 1995, BNR isolate B901 reduced wirestem incidence and area under the disease progress curve (AUDPC) compared with the non-treated control, although not to the level of the fungicide standard, pentachloronitrobenzene (PCNB). In the spring of 1995, all three BNR isolates and PCNB significantly reduced wirestem incidence and AUDPC compared with the non-treated control. Overall disease incidence was low in this season. Marketable weights in some treatments with PDS26E were greater than the non-treated control or PCNB. In the spring of 1996, although no treatments reduced wirestem, PCNB and 232-CG had the highest yields. BNR appears to have the potential to control wirestem on cabbage when low soil temperatures after planting or low precipitation during the growing season limit disease development.}, number={2}, journal={CROP PROTECTION}, author={Ross, RE and Keinath, AP and Cubeta, MA}, year={1998}, month={Mar}, pages={99–104} }
 @article{cubeta_cody_williams_1998, title={First report of Plasmodiophora brassicae on cabbage in eastern North Carolina.}, volume={82}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS.1998.82.1.129D}, abstractNote={ Clubroot, caused by Plasmodiophora brassicae Woronin, has occurred for at least 50 years in three counties in northwestern North Carolina, but has not been reported previously from eastern North Carolina, where most commercial cabbage is produced. In the fall of 1995, clubroot was observed in a direct seeded, commercial cabbage field in Plymouth, NC. Diseased cabbage plants were stunted and roots exhibited clublike swellings. Clubs were randomly harvested from roots of five plants to obtain a composite isolate to determine which race(s) of P. brassicae are infecting cabbage in eastern North Carolina. Three experiments were conducted, using the procedure of Williams (2). Four replicates of 10, 1-week-old seedlings of eight different crucifer cultivars were inoculated by dipping in a spore suspension (1 × 108 cysts/ml) of P. brassicae and planted in pasteurized potting mix. Seedlings dipped in sterile water served as controls. Inoculated seedlings were incubated in a greenhouse at 18 to 28°C for 6 to 8 weeks and assessed for clubroot incidence and severity. The isolate of P. brassicae from eastern North Carolina was most virulent on cabbage (Brassica oleracea var. capitata cv. Jersey Queen), collard (B. oleracea var. acephala cv. Vates), and wild mustard (B. nigra); moderately virulent on canola (B. napus cv. Brutor) and rutabaga (B. napus cvs. Laurentian and Wilhelmsburger); and least virulent on cabbage (cv. Badger Shipper). Canola (B. napus cv. Nevin) and control seedlings were not infected and exhibited no symptoms. Similar results were obtained for all experiments. Based on these results, the isolate of P. brassicae from eastern North Carolina was designated as race 6 and pathotype 5 according to Williams (2) and Some (1), respectively. However, further experiments with single-cyst-derived isolates from individual clubs obtained from different geographic locations are needed to accurately characterize field populations of P. brassicae on cabbage in eastern North Carolina.  References: (1) A. Some et al. Plant Pathol. 45:432, 1996. (2) P. H. Williams. Phytopathology 56:624, 1966. }, number={1}, journal={PLANT DISEASE}, author={Cubeta, MA and Cody, BR and Williams, PH}, year={1998}, month={Jan}, pages={129–129} }
 @article{cubeta_cody_kohli_kohn_1997, title={Clonality in Sclerotinia sclerotiorum on infected cabbage in eastern North Carolina}, volume={87}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.1997.87.10.1000}, abstractNote={ Eighty-four isolates of Sclerotinia sclerotiorum from four cabbage production fields in North Carolina and 16 isolates from an experimental cabbage field plot in Louisiana were DNA-fingerprinted and tested for mycelial compatibility. In a comparison with 594 unique DNA fingerprints of S. sclerotiorum from Canadian canola, no fingerprints were shared among Canadian, North Carolina, and Louisiana populations. DNA fingerprints from the North Carolina sample were distinctive from those of the Canadian and Louisiana samples, with significantly more hybridizing fragments in the 7.7- to 18-kilobase range. Forty-one mycelial compatibility groups (MCGs) and 50 unique DNA fingerprints were identified from the North Carolina sample. Three MCGs and three fingerprints were identified from the Louisiana sample. From the North Carolina sample, 32 MCGs were each associated with a unique fingerprint; of these, there were 11 clones (i.e., cases in which two or more isolates belonged to the same MCG and shared the same DNA fingerprint). Six clones sampled from two or more fields represented approximately 29% of the total sample (24 of 84 isolates), with six clones recovered from fields 75 km apart. There were 10 cases in which one MCG was associated with more than one DNA fingerprint and two cases in which one DNA fingerprint was associated with more than one MCG. The small sample from Louisiana was strictly clonal. The North Carolina sample had a clonal component, but deviated from one-to-one association of MCG with DNA fingerprint to an extent consistent with more recombination or transposition than the other two populations sampled. }, number={10}, journal={PHYTOPATHOLOGY}, author={Cubeta, MA and Cody, BR and Kohli, Y and Kohn, LM}, year={1997}, month={Oct}, pages={1000–1004} }
 @article{mcpartland_vilgalys_cubeta_1997, title={Mushroom poisoning}, volume={55}, number={1997}, journal={American Family Physician}, author={McPartland, J. M. and Vilgalys, R. and Cubeta, M. A.}, year={1997}, pages={1797–1810} }
 @article{mcpartland_cubeta_1997, title={New species, combinations, host associations and location records of fungi associated with hemp (Cannabis sativa)}, volume={101}, ISSN={["0953-7562"]}, DOI={10.1017/S0953756297003584}, abstractNote={Micropeltopsis cannabis sp. nov. and Orbilia luteola (Roum.) comb. nov. are proposed. New Cannabis host associations include binucleate Rhizoctonia spp., Curvularia cymbopogonis, Sphaerotheca macularis, Glomus mosseae, and Pestalotiopsis sp. The geographic ranges of Pseudoperonspora cannabina, Septoria neocannabina and Fusarium graminearum are expanded.}, number={1997 July}, journal={MYCOLOGICAL RESEARCH}, author={McPartland, JM and Cubeta, MA}, year={1997}, month={Jul}, pages={853–857} }
 @article{cubeta_vilgalys_1997, title={Population biology of the Rhizoctonia solani complex}, volume={87}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.1997.87.4.480}, abstractNote={HomePhytopathology®Vol. 87, No. 4Population Biology of the Rhizoctonia solani Complex Previous Symposium OPENOpen Access licensePopulation Biology of the Rhizoctonia solani ComplexM. A. Cubeta and R. VilgalysM. A. CubetaCorresponding author: M. A. Cubeta E-mail address: E-mail Address: [email protected]Search for more papers by this author and R. VilgalysSearch for more papers by this authorAffiliationsAuthors and Affiliations M. A. Cubeta R. Vilgalys Published Online:20 Feb 2007https://doi.org/10.1094/PHYTO.1997.87.4.480AboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat DetailsFiguresLiterature CitedRelated Vol. 87, No. 4 April 1997SubscribeISSN:0031-949Xe-ISSN:1943-7684 Metrics Article History Issue Date: 25 Jan 2008Published: 20 Feb 2007Accepted: 22 Jan 1997 Pages: 480-484 Information© 1997 The American Phytopathological SocietyPDF downloadCited byAdvances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystemFungal Biology Reviews, Vol. 44Identification of a Novel Streptomyces sp. 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Bradley4 November 2019 | Phytopathology®, Vol. 109, No. 12Glasshouse-specific occurrence of basal rot pathogens and the seasonal shift of Rhizoctonia solani anastomosis groups in lettuce14 August 2019 | European Journal of Plant Pathology, Vol. 155, No. 3Genetic and pathogenic variability of Rhizoctonia solani causing crown and root rot on sugar beet in France26 March 2019 | Journal of Plant Pathology, Vol. 101, No. 4Complete Nucleotide Sequence of a Partitivirus from Rhizoctonia solani AG-1 IA Strain C2411 December 2018 | Viruses, Vol. 10, No. 12ROS and trehalose regulate sclerotial development in Rhizoctonia solani AG-1 IAFungal Biology, Vol. 122, No. 5Isolation and Characterization of Extrachromosomal Double-Stranded RNA Elements from Carotenogenic Yeasts15 August 2018Rhizoctonia solani : taxonomy, population biology and management of rhizoctonia seedling disease of soybean2 August 2017 | Plant Pathology, Vol. 67, No. 1Seasonal dynamics and fungicide sensitivity of organisms causing brown patch of tall fescue in North Carolina4 October 2017 | Mycologia, Vol. 32A TaqMan real-time PCR assay for Rhizoctonia cerealis and its use in wheat and soil27 October 2016 | European Journal of Plant Pathology, Vol. 148, No. 2Complete genome sequence of a novel mitovirus from the phytopathogenic fungus Rhizoctonia oryzae-sativae25 January 2017 | Archives of Virology, Vol. 162, No. 5Anastomosis Group and Pathogenicity of Rhizoctonia solani Associated with Stem Canker and Black Scurf of Potato in Heilongjiang Province of China27 January 2017 | American Journal of Potato Research, Vol. 94, No. 2Sensitivity of Rhizoctonia solani to Succinate Dehydrogenase Inhibitor and Demethylation Inhibitor FungicidesOlutoyosi O. Ajayi-Oyetunde, Carolyn J. Butts-Wilmsmeyer, and Carl A. Bradley21 December 2016 | Plant Disease, Vol. 101, No. 3Genetic Structure of Populations of the Wheat Sharp Eyespot Pathogen Rhizoctonia cerealis Anastomosis Group D Subgroup I in ChinaWei Li, Yingpeng Guo, Aixiang Zhang, and Huaigu Chen15 November 2016 | Phytopathology®, Vol. 107, No. 2Identification of a novel mycovirus isolated from Rhizoctonia solani (AG 2-2 IV) provides further information about genome plasticity within the order Tymovirales12 October 2016 | Archives of Virology, Vol. 162, No. 2Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV4 November 2016 | PLOS ONE, Vol. 11, No. 11Characterization of Rhizoctonia solani Associated with Black Scurf in CyprusLoukas Kanetis, Dimitris Tsimouris, and Michalakis Christoforou5 May 2016 | Plant Disease, Vol. 100, No. 8The Relative Importance of Seed- and Soil-Borne Inoculum of Rhizoctonia solani AG-3 in Causing Black Scurf on Potato12 August 2016 | Potato Research, Vol. 59, No. 2Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South AfricaFungal Biology, Vol. 120, No. 5Belowground Defence Strategies Against Rhizoctonia19 November 2016Effects of jinggangmycin on peroxidase and esterase isozymes and phytotoxin from Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. Pirinç kabuğu yanığı nedeni Rhizoctonia solani AG-1 IA tarafından üretilen peroksidaz, esteraz izozimleri ve fitotoksinler üzerinde jinggangmycin etkisiTurkish Journal of Biochemistry, Vol. 41, No. 4Chemische Kontrolle der Späten Rübenfäule in Zuckerrüben1 January 2016 | Sugar IndustryAnastomosis group and pathogenicity of Rhizoctonia solani associated with stem canker and black scurf of potato in China5 May 2015 | European Journal of Plant Pathology, Vol. 143, No. 1Rice WRKY4 acts as a transcriptional activator mediating defense responses toward Rhizoctonia solani, the causing agent of rice sheath blight15 August 2015 | Plant Molecular Biology, Vol. 89, No. 1-2Isolation and characterization of a melanin from Rhizoctonia solani, the causal agent of rice sheath blight20 February 2015 | European Journal of Plant Pathology, Vol. 142, No. 2Possible effects of pathogen inoculation and salicylic acid pre-treatment on the biochemical changes and proline accumulation in green bean17 February 2014 | Archives Of Phytopathology And Plant Protection, Vol. 48, No. 3How many fungi make sclerotia?Fungal Ecology, Vol. 13Propagación in vitro de semillas de la orquídea Comparettia falcata Poepp. & Endl. (Orchidaceae) mediante técnicas simbióticas y asimbióticas20 October 2014 | Acta Agronómica, Vol. 64, No. 2Quantitative methods for assessment of the impact of different crops on the inoculum density of Rhizoctonia solani AG2-2IIIB in soil15 August 2014 | European Journal of Plant Pathology, Vol. 140, No. 4Molecular markers for genotyping anastomosis groups and understanding the population biology of Rhizoctonia species5 July 2014 | Journal of General Plant Pathology, Vol. 80, No. 5In Vitro Fungicide Sensitivity of Rhizoctonia and Waitea Isolates Collected from TurfgrassesJournal of Environmental Horticulture, Vol. 32, No. 3Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species1 August 2014 | American Journal of Botany, Vol. 101, No. 8A novel mycovirus closely related to viruses in the genus Alphapartitivirus confers hypovirulence in the phytopathogenic fungus Rhizoctonia solaniVirology, Vol. 456-457Genetic diversity and population structure of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, in South China19 May 2014 | Canadian Journal of Plant Pathology, Vol. 36, No. 2Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-317 February 2014 | FEMS Microbiology Letters, Vol. 352, No. 2A quitosana como fungistático no crescimento micelial de Rhizoctonia solani KuhnCiência Rural, Vol. 44, No. 1Molecular markers for genotyping anastomosis groups and understanding the population biology of Rhizoctonia species.Japanese Journal of Phytopathology, Vol. 80, No. 100th_AnniversaryDevelopment of SCAR markers and UP-PCR cross-hybridization method for specific detection of four major subgroups of Rhizoctonia from infected turfgrasses20 January 2017 | Mycologia, Vol. 106, No. 1Genetic structure of a population of Rhizoctonia solani AG 2-2 IIIB from Agrostis stolonifera revealed by inter-simple sequence repeat (ISSR) markersCanadian Journal of Plant Pathology, Vol. 35, No. 4Interaction of Sugar Beet Host Resistance and Rhizoctonia solani AG-2-2 IIIB StrainsCarl A. Strausbaugh, Imad A. Eujayl, and Leonard W. Panella8 August 2013 | Plant Disease, Vol. 97, No. 9DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA20 January 2017 | Mycologia, Vol. 105, No. 5The Population Genetic Structure of Rhizoctonia solani AG-3PT from Potato in the Colombian AndesRosa L. Ferrucho, Paulo C. Ceresini, Ursula M. Ramirez-Escobar, Bruce A. McDonald, Marc A. Cubeta, and Celsa García-Domínguez9 July 2013 | Phytopathology®, Vol. 103, No. 8The complete genomic sequence of a novel mycovirus from Rhizoctonia solani AG-1 IA strain B27527 February 2013 | Archives of Virology, Vol. 158, No. 7Genetic structure of populations of Rhizoctonia solani AG-4 from five provinces in Iran2 August 2012 | Plant Pathology, Vol. 62, No. 3Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsiiEfrén Remesal, Blanca B. Landa, María del Mar Jiménez-Gasco, and Juan A. Navas-Cortés11 April 2013 | Phytopathology®, Vol. 103, No. 5Chemotaxonomy of fungi in the Rhizoctonia solani species complex performing GC/MS metabolite profiling30 July 2011 | Metabolomics, Vol. 9, No. S1Selection for Resistance to the Rhizoctonia-Bacterial Root Rot Complex in Sugar BeetCarl A. Strausbaugh, Imad A. Eujayl, and Paul Foote7 December 2012 | Plant Disease, Vol. 97, No. 1Mechanism of the Generation of New Somatic Compatibility Groups within Thanatephorus cucumeris (Rhizoctonia solani)Microbes and Environments, Vol. 28, No. 3Efeito da quitosana na emergência, desenvolvimento inicial e caracterização bioquímica de plântulas de Acacia mearnsiiRevista Árvore, Vol. 36, No. 6Cloning and functional analysis of an endo-PG-encoding gene Rrspg1 of Rhizoctonia solani , the causal agent of rice sheath blightCanadian Journal of Plant Pathology, Vol. 34, No. 3Microorganisms Associated with Valencia Peanut Affected by Pod Rot in New MexicoPeanut Science, Vol. 39, No. 2Rhizoctonia Web Blight—A New Disease on Mint in IsraelNadav Nitzan, David Chaimovitsh, Rachel Davidovitch-Rekanati, Michal Sharon, and Nativ Dudai8 February 2012 | Plant Disease, Vol. 96, No. 3Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers16 February 2012 | Journal of General Plant Pathology, Vol. 78, No. 2Drycore Appears to Result from an Interaction between Rhizoctonia solani and Wireworm (Agriotes ssp.)—Evidence from a 3-Year Field Survey18 March 2012 | Potato Research, Vol. 55, No. 1Morphological and pathological variations of rice sheath blight inciting south Indian Rhizoctonia solani isolatesArchives Of Phytopathology And Plant Protection, Vol. 45, No. 4Isolation and Characterization of Extrachromosomal Double-Stranded RNA Elements in Xanthophyllomyces dendrorhous19 May 2012Establishment of Agrobacterium tumefaciens- Mediated Transformation System for Rice Sheath Blight Pathogen Rhizoctonia solaniRice Science, Vol. 18, No. 4Virulence, distribution and diversity of Rhizoctonia solani from sugar beet in Idaho and OregonCanadian Journal of Plant Pathology, Vol. 33, No. 26 Mating Type in Basidiomycetes: Unipolar, Bipolar, and Tetrapolar Patterns of Sexuality10 June 2011Characterization of Rhizoctonia spp. Isolates Associated with Damping-Off Disease in Cotton and Tobacco Seedlings in GreeceC. Bacharis, A. Gouziotis, P. Kalogeropoulou, O. Koutita, K. Tzavella-Klonari, and G. S. Karaoglanidis6 October 2010 | Plant Disease, Vol. 94, No. 11Molecular and Conventional Identification and Pathogenicity of Rhizoctonia solani Isolates from Tobacco (Nicotiana tabacum L.) in Samsun, Turkey1 April 2009 | Journal of Phytopathology, Vol. 157, No. 11-12Genetic Structure of Populations of the Rice-Infecting Pathogen Rhizoctonia solani AG-1 IA from ChinaJoana Bernardes-de-Assis, Michelangelo Storari, Marcello Zala, Wenxiang Wang, Daohong Jiang, Li ShiDong, Meisong Jin, Bruce A. McDonald, and Paulo C. Ceresini11 August 2009 | Phytopathology®, Vol. 99, No. 9Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani16 July 2009 | Journal of Molecular Evolution, Vol. 69, No. 2Characterisation of fungal pathogens causing basal rot of lettuce in Belgian greenhouses24 October 2008 | European Journal of Plant Pathology, Vol. 124, No. 1Identification of sugar beet germplasm EL51 as a source of resistance to post-emergence Rhizoctonia damping-off21 October 2008 | European Journal of Plant Pathology, Vol. 123, No. 4Heterokaryon formation in Thanatephorus cucumeris (Rhizoctonia solani) AG-1 ICMycological Research, Vol. 112, No. 9Genetic Structure of Populations of Rhizoctonia solani Anastomosis Group-1 IA from Soybean in BrazilM. B. Ciampi, M. C. Meyer, M. J. N. Costa, M. Zala, B. A. McDonald, and P. C. Ceresini11 July 2008 | Phytopathology®, Vol. 98, No. 8Use of single-protoplast isolates in the study of the mating phenomena of Rhizoctonia solani (Thanatephorus cucumeris) AG-1 IC and IAMycoscience, Vol. 49, No. 2Phylogenetic analysis of Rhizoctonia solani subgroups associated with web blight symptoms on common bean based on ITS-5.8S rDNA5 December 2007 | Journal of General Plant Pathology, Vol. 74, No. 1Cross-pathogenicity of Rhizoctonia solani strains on pasture legumes in pasture-crop rotations28 November 2007 | Plant and Soil, Vol. 302, No. 1-2Reação de cultivares de feijão-caupi à mela (Rhizoctonia solani) em RoraimaFitopatologia Brasileira, Vol. 32, No. 5Incompatibilidade somática em Rhizoctonia solani AG-1 IA da sojaSumma Phytopathologica, Vol. 32, No. 3Diversidade genética de isolados de Rhizoctonia solani coletados em feijão-caupi no Estado de RoraimaFitopatologia Brasileira, Vol. 31, No. 3Double-stranded RNA: distribution and analysis among isolates of Rhizoctonia solani AG-2 to -13Plant Pathology, Vol. 54, No. 2Morphological and molecular characterization of mycorrhizal fungi isolated from neotropical orchids in BrazilCanadian Journal of Botany, Vol. 83, No. 1Differences in mycorrhizal preferences between two tropical orchids16 June 2004 | Molecular Ecology, Vol. 13, No. 8Molecular Characterization of Rhizoctonia solaniGenetic diversity in potato field populations of Thanatephorus cucumeris AG-3, revealed by ITS polymorphism and RAPD markersMycological Research, Vol. 107, No. 11Genetic Variation Among Isolates of the Web Blight Pathogen of Common Bean Based on PCR-RFLP of the ITS-rDNA RegionG. Godoy-Lutz, J. R. Steadman, B. Higgins, and K. Powers23 February 2007 | Plant Disease, Vol. 87, No. 7Genetic diversity and virulence of Rhizoctonia species associated with plantings of Lotus corniculatusMycological Research, Vol. 107, No. 2Diversity and host specificity of endophytic Rhizoctonia ‐like fungi from tropical orchids1 November 2002 | American Journal of Botany, Vol. 89, No. 11Genetic diversity of Rhizoctonia solani AG-3 from potato and tobacco in North Carolina31 January 2017 | Mycologia, Vol. 94, No. 3Genetic structure of populations of Rhizoctonia solani AG-3 on potato in eastern North Carolina31 January 2017 | Mycologia, Vol. 94, No. 3RAPD Analysis of Indian Isolates of Rice Sheath Blight Fungus Rhizoctonia solani30 December 2012 | Journal of Plant Biochemistry and Biotechnology, Vol. 11, No. 1Hyphal Anastomosis Reactions, rDNA-Internal Transcribed Spacer Sequences, and Virulence Levels Among Subsets of Rhizoctonia solani Anastomosis Group-2 (AG-2) and AG-BID. E. Carling, S. Kuninaga, and K. A. Brainard22 February 2007 | Phytopathology®, Vol. 92, No. 1Double-stranded RNA elements in Rhizoctonia solani AG 3Mycological Research, Vol. 106, No. 1Mycologia, Vol. 94, No. 2Protoplast preparation and transient transformation of Rhizoctonia solaniMycological Research, Vol. 105, No. 11Mycological Research NewsMycological Research, Vol. 104, No. 7High Levels of Gene Flow and Heterozygote Excess Characterize Rhizoctonia solani AG-1 IA (Thanatephorus cucumeris) from TexasFungal Genetics and Biology, Vol. 28, No. 3Characterization of Mycorrhizal Isolates of Rhizoctonia solani from an Orchid, Including AG-12, a New Anastomosis GroupD. E. Carling, E. J. Pope, K. A. Brainard, and D. A. Carter22 February 2007 | Phytopathology®, Vol. 89, No. 10Evidence for segregation of somatic incompatibility during hyphal tip subculture of Rhizoctonia solani AG 4Mycological Research, Vol. 103, No. 10T HE E VOLUTION OF A SEXUAL F UNGI : Reproduction, Speciation and ClassificationAnnual Review of Phytopathology, Vol. 37, No. 1Microscopic observation of perfect hyphal fusion in Rhizoctonia solaniMycological Research, Vol. 103, No. 4Characterization of Rhizoctonia solani Isolates from Tobacco Fields Related to Anastomosis Groups 2-1 and BI (AG 2-1 and AG BI)Journal of Phytopathology, Vol. 147, No. 2Polymerase chain reaction-based assay for specific detection of Rhizoctonia solani AG-3 isolatesMycological Research, Vol. 103, No. 1One stop mycologyMycological Research, Vol. 103, No. 1Somatic Incompatibility in Fungi}, number={4}, journal={PHYTOPATHOLOGY}, author={Cubeta, MA and Vilgalys, R}, year={1997}, month={Apr}, pages={480–484} }
 @article{subbiah_riddick_peele_reynolds_cubeta_1996, title={First report of Fusarium oxysporum on clary sage in North America}, volume={80}, number={9}, journal={Plant Disease}, author={Subbiah, V. and Riddick, M. and Peele, D. and Reynolds, R.J. and Cubeta, M.A.}, year={1996}, pages={1080} }
 @inbook{cubeta_vilgalys_gonzalez_1996, title={Molecular Analysis of Ribosomal RNA Genes in Rhizoctonia Fungi}, ISBN={9789048145973 9789401729017}, url={http://dx.doi.org/10.1007/978-94-017-2901-7_7}, DOI={10.1007/978-94-017-2901-7_7}, booktitle={Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control}, publisher={Springer Netherlands}, author={Cubeta, Marc A. and Vilgalys, Rytas and Gonzalez, Dolores}, year={1996}, pages={81–86} }
 @article{vilgalys_cubeta_1994, title={Molecular Systematics and Population Biology of Rhizoctonia}, volume={32}, ISSN={0066-4286 1545-2107}, url={http://dx.doi.org/10.1146/annurev.py.32.090194.001031}, DOI={10.1146/annurev.py.32.090194.001031}, abstractNote={Fungi classified as Rhizoctonia species represent an amalgam of taxonomically diverse groups that differ in many significant features, including their sexual stages (teleomorph), asexual stages (anamoI]'lh), and other characters (101, 106, 107). Because of the importance of many Rhizoctonia species as plant pathogens, a variety of useful approaches have been developed for identifying many groups of Rhizoctonia spp. based on ultrastructural features, information from teleomorphs, anastomosis behavior, and molecular biology. This review summarizes recent progress in understanding patterns of genetic diversity revealed through application of molecular data, and the relation of genetic diversity to the taxonomy and population biology of Rhizoctonia. Several reviews have summarized the most current framework for under­ standing diversity within Rhizoctonia , including the R. solani complex (79), binucleate Rhizoctonia (48), and other Rhizoctonia (101). Most Rhizoctonia can now usually be classified into major groups based on teleomorph associ­ ation, as well as into more narrowly defined intraspecific groups (1, 5,79). Progress in understanding the biology and pathology of Rhizoctonia can be traced to the realization that genetically diverse groups exist at several levels of organization:}, number={1}, journal={Annual Review of Phytopathology}, publisher={Annual Reviews}, author={Vilgalys, R and Cubeta, M A}, year={1994}, month={Sep}, pages={135–155} }
 @article{cubeta_briones-ortega_vilgalys_1993, title={Reassessment of Heterokaryon Formation in Rhizoctonia Solani Anastomosis Group 4}, volume={85}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/00275514.1993.12026332}, DOI={10.1080/00275514.1993.12026332}, abstractNote={ABSTRACTMating compatibility reactions were tested using homokaryotic strains belonging to anastomosis group 4 in the Rhizoctonia solani complex. Previous studies on mating patterns employed tuft f...}, number={5}, journal={Mycologia}, publisher={Informa UK Limited}, author={Cubeta, M. A. and Briones-Ortega, R. and Vilgalys, R.}, year={1993}, month={Sep}, pages={777–787} }
 @article{cubeta_echandi_1991, title={Biological Control of Rhizoctonia and Pythium Damping-Off of Cucumber: An Integrated Approach}, volume={1}, ISSN={["1049-9644"]}, DOI={10.1016/1049-9644(91)90071-7}, abstractNote={Binucleate Rhizoctonia spp. were evaluated singly and in combination with seed treated with selected biocontrol bacteria, fungicides, or osmopriming agents in the greenhouse and field for control of Rhizoctonia and Pythium damping-off of cucumber. In the greenhouse, in a pasteurized soil mix, treatments with 8 of 19 isolates of binucleate Rhizoctonia spp. yielded decreased (P = 0.05) levels of preemergence damping-off caused by R. solani. Osmopriming cucumber seed with KNO3, NaCl, or polyethylene glycol (PEG 8000) did not protect cucumber from Rhizoctonia and Pythium damping-off in naturally infested soil in the greenhouse. Treating cucumber seed with strain E6, ECH, and ECT of Enterobacter cloacae and sowing in soil alone or in soil amended with isolate 232-CG of binucleate Rhizoctonia sp. resulted in decreased (P = 0.05) levels of Rhizoctonia and Pythium preemergence damping-off in naturally infested soil in the greenhouse but not in the field. Amendment of isolate 232-CG to soil and combining it with seed treatment or soil application of metalaxyl produced decreased (P = 0.05) levels of Rhizoctonia and Pythium preemergence damping-off in 12 naturally infested fields at three geographic locations when compared with nontreated seed sown in soil alone or in soil amended with isolate 232-CG alone. Seed treated with metalaxyl and sown in soil amended with isolate 232-CG developed decreased (P = 0.05) levels of Rhizoctonia and Pythium preemergence damping-off at 20 and 30% of the field sites compared to seed treated with captan and metalaxyl, respectively. However, seed treated with metalaxyl or captan had higher (P = 0.05) disease incidence of Rhizoctonia at 20 and 60% of the field sites, respectively, when compared to seed treated with metalaxyl and sown in soil amended with isolate 232-CG. Control of cucumber damping-off caused by R. solani and Pythium spp. requires an integrated approach and can be achieved using the binucleate Rhizoctonia sp. isolate 232-CG combined with the fungicide metalaxyl. This treatment protected cucumber from Rhizoctonia and Pythium damping-off as effectively as the recommended fungicide captan.}, number={3}, journal={BIOLOGICAL CONTROL}, author={Cubeta, M. A. and Echandi, E.}, year={1991}, month={Oct}, pages={227–236} }
 @article{cubeta_echandi_abernethy_vilgalys_1991, title={CHARACTERIZATION OF ANASTOMOSIS GROUPS OF BINUCLEATE RHIZOCTONIA SPECIES USING RESTRICTION ANALYSIS OF AN AMPLIFIED RIBOSOMAL-RNA GENE}, volume={81}, ISSN={["1943-7684"]}, DOI={10.1094/Phyto-81-1395}, abstractNote={Seven U.S. and 16 Japanese binucleate Rhizoctonia anastomosis tester isolates, representing 21 different anastomosis groups, were characterized by restriction analysis of a ribosomal RNA (rRNA) gene. Genomic DNA was extracted from each isolate and a region of DNA coding for a portion of the 25S rRNA (rDNA) was amplified using the polymerase chain reaction. Five tester isolates (CAG1, AGF, AGI, AGJ, and AGK) produced either two or three bands ranging from 1.4 to 1.8 kilobases (kb), whereas five other tester isolates (CAG5, AGBa, AGC, AGD, and AGH) produced a single, 1.8-kb fragment (...)}, number={11}, journal={PHYTOPATHOLOGY}, author={CUBETA, MA and ECHANDI, E and ABERNETHY, T and VILGALYS, R}, year={1991}, month={Nov}, pages={1395–1400} }
 @article{cubeta_echandi_gumpertz_1991, title={Survival of Binucleate Rhizoctonia Species, Biological Control Agents, in Soil and Plant Debris under Field Conditions}, volume={1}, ISSN={["1090-2112"]}, DOI={10.1016/1049-9644(91)90070-g}, abstractNote={Survival of binucleate zoctoniaspp. (isolates 232-CG and JF-3N1-1) was studied in soil under field conditions. Oat kernels colonized with 232-CG and JF-3N11 were finely ground and buried 1, 15, and 30 cm deep in two field soils at Clayton (CL) and Raleigh (RA), North Carolina, and sampled monthly for 1 year. After burial for 1 month in RA soil, populations of 232-CG and JF-3N1-1 increased 49 and 29%, respectively, at 1 cm, but decreased 6 to 67% at 15 and 30 cm. Neither isolate was recovered after 5 months at 30 cm or after 7 months at 1 and 15 cm in RA soil. Populations of 232-CG and JF-3N1-1 increased 19 and 58%, respectively, after 1 month at 1 cm in CL soil, but populations of both isolates decreased between 38 and 69% after 1 month at 15 and 30 cm. Neither isolate was recovered after 9 months in CL soil. Snapbean stems colonized with 232-CG and JF-3N1-1 were buried 1 and 15 cm deep in field soils at CL and RA and were also sampled monthly for 1 year. Recovery of 232-CG and JF-3N1-1 from precolonized snapbean stems decreased by 50% after 1 month at 1 and 15 cm in CL and RA soils. After 2 and 3 months at both depths, recovery of 232-CG and JF-3N1-1 increased 10 to 40% and was followed by an irregular and gradual decline in RA soil. Recovery of 232-CG was higher (P < 0.02) than that of JF-3N1-1 at both depths in RA soil. Recovery of 232-CG (y = 0.71 − 0.11x) and JF-3N1-1 (y = 0.61 − 0.10x) decreased over time at a similar rate, as did the recovery of both isolates from 1-cm (y = 0.58 − 0.11x) and 15-cm (y = 0.65 − 0.10x) depths. After 2 months at 1 and 15 cm in CL soil, recovery of 232-CG increased 30 and 3%, respectively, while recovery of JF-3N1-1 decreased 35 and 10%, respectively, and then decreased gradually after 3 months. Recovery of 232-CG (y = 0.77 − 0.13x) and JF-3N1-1 (y = 0.51 − 0.10x) decreased at different rates over time as did the recovery of both isolates from 1-cm (y = 0.74 − 0.13x) and 15-cm (y = 0.64 − 0.10x) depths. Recovery of both isolates was higher (P = 0.001) at 15 cm than at 1 cm and neither isolate was recovered after 11 months in CL and RA soils. Thus, survival of isolates 232-CG and JF-3N1-1 of the binucleate Rhizoctonia spp. in field soil was dependent on the method of their amendments to soil (colonized oat kernels vs. snapbean stems) and the length of burial in the soil (1 cm vs. 15 cm). With this information it may be possible to introduce binucleate Rhizoctonia spp. in soil and implement strategies for the management and maintenance of adequate populations of these biological control agents to control diseases caused by R. solani.}, number={3}, journal={BIOLOGICAL CONTROL}, author={Cubeta, M. A. and Echandi, E. and Gumpertz, M. L.}, year={1991}, month={Oct}, pages={218–226} }
 @article{cubeta_hartman_sinclair_1985, title={Interaction between Bacillus subtilis and fungi associated with soybean seeds}, volume={69}, journal={Plant Disease}, author={Cubeta, M.A. and Hartman, G.L. and Sinclair, J.B.}, year={1985}, pages={506–509} }