@article{saffer_tateosian_saville_yang_ristaino_2024, title={Reconstructing historic and modern potato late blight outbreaks using text analytics}, volume={14}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-024-52870-2}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Saffer, Ariel and Tateosian, Laura and Saville, Amanda C. and Yang, Yi-Peng and Ristaino, Jean B.}, year={2024}, month={Feb} }
 @article{lee_hossain_jamalzadegan_liu_wang_saville_shymanovich_paul_rotenberg_whitfield_et al._2023, title={Abaxial leaf surface-mounted multimodal wearable sensor for continuous plant physiology monitoring}, volume={9}, ISSN={["2375-2548"]}, DOI={10.1126/sciadv.ade2232}, abstractNote={Wearable plant sensors hold tremendous potential for smart agriculture. We report a lower leaf surface-attached multimodal wearable sensor for continuous monitoring of plant physiology by tracking both biochemical and biophysical signals of the plant and its microenvironment. Sensors for detecting volatile organic compounds (VOCs), temperature, and humidity are integrated into a single platform. The abaxial leaf attachment position is selected on the basis of the stomata density to improve the sensor signal strength. This versatile platform enables various stress monitoring applications, ranging from tracking plant water loss to early detection of plant pathogens. A machine learning model was also developed to analyze multichannel sensor data for quantitative detection of tomato spotted wilt virus as early as 4 days after inoculation. The model also evaluates different sensor combinations for early disease detection and predicts that minimally three sensors are required including the VOC sensors.}, number={15}, journal={SCIENCE ADVANCES}, author={Lee, Giwon and Hossain, Oindrila and Jamalzadegan, Sina and Liu, Yuxuan and Wang, Hongyu and Saville, Amanda C. and Shymanovich, Tatsiana and Paul, Rajesh and Rotenberg, Dorith and Whitfield, Anna E. and et al.}, year={2023}, month={Apr} }
 @article{coomber_saville_carbone_ristaino_2023, title={An open-access T-BAS phylogeny for emerging Phytophthora species}, volume={18}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0283540}, DOI={10.1371/journal.pone.0283540}, abstractNote={Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.}, number={4}, journal={PLOS ONE}, author={Coomber, Allison and Saville, Amanda and Carbone, Ignazio and Ristaino, Jean Beagle}, editor={Blair, Jaime E.Editor}, year={2023}, month={Apr} }
 @article{saville_mcgrath_jones_polo_ristaino_2023, title={Understanding the Genotypic and Phenotypic Structure and Impact of Climate on <i>Phytophthora nicotianae</i> Outbreaks on Potato and Tomato in the Eastern United States}, volume={113}, ISSN={["1943-7684"]}, url={http://dx.doi.org/10.1094/phyto-11-22-0411-r}, DOI={10.1094/PHYTO-11-22-0411-R}, abstractNote={ Samples from potato fields with lesions with late blight-like symptoms were collected from eastern North Carolina in 2017 and the causal agent was identified as Phytophthora nicotianae. We have identified P. nicotianae in potato and tomato samples from North Carolina, Virginia, Maryland, Pennsylvania, and New York. Ninety-two field samples were collected from 46 fields and characterized for mefenoxam sensitivity, mating type, and simple sequence repeat genotype using microsatellites. Thirty-two percent of the isolates were the A1 mating type, while 53% were the A2 mating type. In six cases, both A1 and A2 mating types were detected in the same field in the same year. All isolates tested were sensitive to mefenoxam. Two genetic groups were discerned based on STRUCTURE analysis: one included samples from North Carolina and Maryland, and one included samples from all five states. The data suggest two different sources of inoculum from the field sites sampled. Multiple haplotypes within a field and the detection of both mating types in close proximity suggests that P. nicotianae may be reproducing sexually in North Carolina. There was a decrease in the average number of days with weather suitable for late blight, from 2012 to 2016 and 2017 to 2021 in all of the North Carolina counties where P. nicotianae was reported. P. nicotianae is more thermotolerant than P. infestans and grows at higher temperatures (25 to 35°C) than P. infestans (18 to 22°C). Late blight outbreaks have decreased in recent years and first reports of disease are later, suggesting that the thermotolerant P. nicotianae may cause more disease as temperatures rise due to climate change. }, number={8}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Saville, Amanda C. and McGrath, Margaret T. and Jones, Chris and Polo, John and Ristaino, Jean B.}, year={2023}, month={Aug}, pages={1506–1514} }
 @article{saville_ristaino_2021, title={Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents}, volume={11}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-021-90937-6}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Saville, Amanda C. and Ristaino, Jean B.}, year={2021}, month={Jun} }
 @article{paul_ostermann_chen_saville_yang_gu_whitfield_ristaino_wei_2021, title={Integrated microneedle-smartphone nucleic acid amplification platform for in-field diagnosis of plant diseases}, volume={187}, ISSN={["1873-4235"]}, url={https://doi.org/10.1016/j.bios.2021.113312}, DOI={10.1016/j.bios.2021.113312}, abstractNote={We demonstrate an integrated microneedle (MN)-smartphone nucleic acid amplification platform for “sample-to-answer” diagnosis of multiplexed plant pathogens within 30 min. This portable system consists of a polymeric MN patch for rapid nucleic acid extraction within a minute and a 3D-printed smartphone imaging device for loop-mediated isothermal amplification (LAMP) reaction and detection. We expanded the extraction of the MN technology for DNA targets as in the previous study (ACS Nano, 2019, 13, 6540–6549) to more fragile RNA biomarkers, evaluated the storability of the extracted nucleic acid samples on MN surfaces, and developed a smartphone-based LAMP amplification and fluorescent reader device that can quantify four LAMP reactions on the same chip. In addition, we have found that the MN patch containing as few as a single needle tip successfully extracted enough RNA for RT-PCR or RT-LAMP analysis. Moreover, MN-extracted RNA samples remained stable on MN surfaces for up to three days. The MN-smartphone platform has been used to detect both Phytophthora infestans DNA and tomato spotted wilt virus (TSWV) RNA down to 1 pg, comparable to the results from a benchtop thermal cycler. Finally, multiplexed detection of P. infestans and TSWV through a single extraction from infected tomato leaves and amplification on the smartphone without benchtop equipment was demonstrated.}, journal={BIOSENSORS & BIOELECTRONICS}, publisher={Elsevier BV}, author={Paul, Rajesh and Ostermann, Emily and Chen, Yuting and Saville, Amanda C. and Yang, Yuming and Gu, Zhen and Whitfield, Anna E. and Ristaino, Jean B. and Wei, Qingshan}, year={2021}, month={Sep} }
 @article{saville_la spada_faedda_migheli_scanu_ermacora_gilardi_fedele_rossi_lenzi_et al._2021, title={Population structure of Phytophthora infestans collected on potato and tomato in Italy}, volume={8}, ISSN={["1365-3059"]}, DOI={10.1111/ppa.13444}, abstractNote={Abstract}, journal={PLANT PATHOLOGY}, author={Saville, Amanda C. and La Spada, Federico and Faedda, Roberto and Migheli, Quirico and Scanu, Bruno and Ermacora, Paolo and Gilardi, Giovanna and Fedele, Giorgia and Rossi, Vitorrio and Lenzi, Nicolo and et al.}, year={2021}, month={Aug} }
 @article{ristaino_saville_paul_cooper_wei_2020, title={Detection of Phytophthora infestans by Loop-Mediated Isothermal Amplification, Real-Time LAMP, and Droplet Digital PCR}, volume={104}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-06-19-1186-RE}, abstractNote={ Phytophthora infestans is the causal agent of potato late blight, a devastating disease of tomato and potato and a threat to global food security. Early detection and intervention is essential for effective management of the pathogen. We developed a loop-mediated isothermal amplification (LAMP) assay for P. infestans and compared this assay to conventional PCR, real-time LAMP, and droplet digital PCR for detection of P. infestans. The LAMP assay was specific for P. infestans on potato and tomato and did not amplify other potato- or tomato-infecting Phytophthora species or other fungal and bacterial pathogens that infect potato and tomato. The detection threshold for SYBR Green LAMP and real-time LAMP read with hydroxynaphthol blue and EvaGreen was 1 pg/µl. In contrast, detection by conventional PCR was 10 pg/µl. Droplet digital PCR had the lowest detection threshold (100 fg/µl). We adapted the LAMP assay using SYBR Green and a mobile reader (mReader) for use in the field. Detection limits were 584 fg/µl for SYBR Green LAMP read on the mReader, which was more sensitive than visualization with the human eye. The mobile platform records geospatial coordinates and data from positive pathogen detections can be directly uploaded to a cloud database. Data can then be integrated into disease surveillance networks. This system will be useful for real-time detection of P. infestans and will improve the timeliness of reports into surveillance systems such as USABlight or EuroBlight. }, number={3}, journal={PLANT DISEASE}, author={Ristaino, Jean B. and Saville, Amanda C. and Paul, Rajesh and Cooper, Donald C. and Wei, Qingshan}, year={2020}, month={Mar}, pages={708–716} }
 @article{paul_saville_hansel_ye_ball_williams_chang_chen_gu_ristaino_et al._2019, title={Extraction of Plant DNA by Microneedle Patch for Rapid Detection of Plant Diseases}, volume={13}, ISSN={1936-0851 1936-086X}, url={http://dx.doi.org/10.1021/acsnano.9b00193}, DOI={10.1021/acsnano.9b00193}, abstractNote={In-field molecular diagnosis of plant diseases via nucleic acid amplification is currently limited by cumbersome protocols for extracting and isolating pathogenic DNA from plant tissues. To address this challenge, a rapid plant DNA extraction method was developed using a disposable polymeric microneedle (MN) patch. By applying MN patches on plant leaves, amplification-assay-ready DNA can be extracted within a minute from different plant species. MN-extracted DNA was used for direct polymerase chain reaction amplification of plant plastid DNA without purification. Furthermore, using this patch device, extraction of plant pathogen DNA ( Phytophthora infestans) from both laboratory-inoculated and field-infected leaf samples was performed for detection of late blight disease in tomato. MN extraction achieved 100% detection rate of late blight infections for samples after 3 days of inoculation when compared to the conventional gold standard cetyltrimethylammonium bromide (CTAB)-based DNA extraction method and 100% detection rate for all blind field samples tested. This simple, cell-lysis-free, and purification-free DNA extraction method could be a transformative approach to facilitate rapid sample preparation for molecular diagnosis of various plant diseases directly in the field.}, number={6}, journal={ACS Nano}, publisher={American Chemical Society (ACS)}, author={Paul, Rajesh and Saville, Amanda C. and Hansel, Jeana C. and Ye, Yanqi and Ball, Carmin and Williams, Alyssa and Chang, Xinyuan and Chen, Guojun and Gu, Zhen and Ristaino, Jean B. and et al.}, year={2019}, month={Jun}, pages={6540–6549} }
 @article{saville_ristaino_2019, title={Genetic Structure and Subclonal Variation of Extant and Recent U.S. Lineages of Phytophthora infestans}, volume={109}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-09-18-0357-R}, DOI={10.1094/PHYTO-09-18-0357-R}, abstractNote={ The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century U.S. lineages of P. infestans and compared them with populations from South America and Mexico to examine genetic relationships and potential sources of lineages. US-23, currently the most prevalent lineage detected in the United States, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other U.S. lineages. Many of the other U.S. lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from simple sequence repeat genotype datasets from USABlight outbreaks clearly showed the expansion of US-23 over a 6-year time period and geographic substructuring of some lineages in the western United States. Many clonal lineages of P. infestans in the United States have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources. }, number={9}, journal={Phytopathology}, publisher={Scientific Societies}, author={Saville, Amanda and Ristaino, Jean Beagle}, year={2019}, month={Sep}, pages={1614–1627} }
 @article{liu_langemeier_small_joseph_fry_ristaino_saville_gramig_preckel_2018, title={A Risk Analysis of Precision Agriculture Technology to Manage Tomato Late Blight}, volume={10}, ISSN={["2071-1050"]}, DOI={10.3390/su10093108}, abstractNote={Precision agriculture technology can transform farming related data into useful information, which may lead to more efficient usage of agricultural resources and increase sustainability. This paper compares precision agriculture technology with traditional practices in scheduling fungicide application so as to manage late blight disease in tomato production. The following three fungicide scheduling strategies were evaluated: a calendar-based strategy, the BlightPro Decision Support System based strategy (DSS-based strategy), and a strategy that does not involve fungicide application. The data from field trials and computer simulation experiments were used to construct distributions of the net return per acre for the calendar-based and the DSS-based strategies. These distributions were then compared using three standard approaches to ranking risky alternatives, namely: stochastic dominance, stochastic dominance with respect to a function, and stochastic efficiency with respect to a function. Assuming no yield differences between the calendar-based and the DSS-based strategies, the calendar-based strategy was preferred for highly late blight susceptible cultivars, and the DSS-based strategy was preferred for moderately susceptible and moderately resistant cultivars. Assuming no yield differences, the value of the BlightPro Decision Support System ranged from −$28 to $48 per acre. With the yield improvement for the DSS-based strategy included, the DSS-based strategy was preferred for the cultivars in all of the disease-resistance categories with the value ranging from $496 to $1714 per acre.}, number={9}, journal={SUSTAINABILITY}, author={Liu, Yangxuan and Langemeier, Michael R. and Small, Ian M. and Joseph, Laura and Fry, William E. and Ristaino, Jean B. and Saville, Amanda and Gramig, Benjamin M. and Preckel, Paul V.}, year={2018}, month={Sep} }
 @article{dey_saville_myers_tewari_cooke_tripathy_fry_ristaino_guha roy_2018, title={Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-018-22192-1}, DOI={10.1038/s41598-018-22192-1}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Dey, Tanmoy and Saville, Amanda and Myers, Kevin and Tewari, Susanta and Cooke, David E. L. and Tripathy, Sucheta and Fry, William E. and Ristaino, Jean B. and Guha Roy, Sanjoy}, year={2018}, month={Mar} }
 @article{saville_charles_chavan_muñoz_gómez-alpizar_ristaino_2017, title={Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations}, volume={107}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/PHYTO-02-17-0045-R}, DOI={10.1094/phyto-02-17-0045-r}, abstractNote={ Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas. }, number={12}, journal={Phytopathology}, publisher={Scientific Societies}, author={Saville, Amanda and Charles, Melodi and Chavan, Suchitra and Muñoz, Miguel and Gómez-Alpizar, Luis and Ristaino, Jean Beagle}, year={2017}, month={Dec}, pages={1541–1548} }
 @article{saville_martin_ristaino_2016, title={Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary}, volume={11}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0168381}, DOI={10.1371/journal.pone.0168381}, abstractNote={Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, was responsible for the Irish potato famine of the 1840s. Initial disease outbreaks occurred in the US in 1843, two years prior to European outbreaks. We examined the evolutionary relationships and source of the 19th-century outbreaks using herbarium specimens of P. infestans from historic (1846–1970) and more recent isolates (1992–2014) of the pathogen. The same unique SSR multilocus genotype, named here as FAM-1, caused widespread outbreaks in both US and Europe. The FAM-1 lineage shared allelic diversity and grouped with the oldest specimens collected in Colombia and Central America. The FAM-1 lineage of P. infestans formed a genetic group that was distinct from more recent aggressive lineages found in the US. The US-1 lineage formed a second, mid-20th century group. Recent modern US lineages and the oldest Mexican lineages formed a genetic group with recent Mexican lineages, suggesting a Mexican origin of recent US lineages. A survey of mitochondrial haplotypes in a larger set of global herbarium specimens documented the more frequent occurrence of the HERB-1 (type Ia) mitochondrial haplotype in archival collections from 1866–75 and 1906–1915 and the rise of the Ib mitochondrial lineage (US-1) between 1946–1955. The FAM-1 SSR lineage survived for almost 100 years in the US, was geographically widespread, and was displaced first in the mid-20th century by the US-1 lineage and then by distinct new aggressive lineages that migrated from Mexico.}, number={12}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Saville, Amanda C. and Martin, Michael D. and Ristaino, Jean B.}, editor={Gijzen, MarkEditor}, year={2016}, month={Dec}, pages={e0168381} }
 @article{saville_graham_gruenwald_myers_fry_ristaino_2015, title={Fungicide Sensitivity of US Genotypes of Phytophthora infestans to Six Oomycete-Targeted Compounds}, volume={99}, ISSN={["1943-7692"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84930615057&partnerID=MN8TOARS}, DOI={10.1094/pdis-05-14-0452-re}, abstractNote={ Phytophthora infestans causes potato late blight, an important and costly disease of potato and tomato crops. Seven clonal lineages of P. infestans identified recently in the United States were tested for baseline sensitivity to six oomycete-targeted fungicides. A subset of the dominant lineages (n = 45) collected between 2004 and 2012 was tested in vitro on media amended with a range of concentrations of either azoxystrobin, cyazofamid, cymoxanil, fluopicolide, mandipropamid, or mefenoxam. Dose-response curves and values for the effective concentration at which 50% of growth was suppressed were calculated for each isolate. The US-8 and US-11 clonal lineages were insensitive to mefenoxam while the US-20, US-21, US-22, US-23, and US-24 clonal lineages were sensitive to mefenoxam. Insensitivity to azoxystrobin, cyazofamid, cymoxanil, fluopicolide, or mandipropamid was not detected within any lineage. Thus, current U.S. populations of P. infestans remained sensitive to mefenoxam during the displacement of the US-22 lineage by US-23 over the past 5 years. }, number={5}, journal={PLANT DISEASE}, author={Saville, Amanda and Graham, Kim and Gruenwald, Niklaus J. and Myers, Kevin and Fry, William E. and Ristaino, Jean Beagle}, year={2015}, month={May}, pages={659–666} }
 @article{lassiter_russ_nusbaum_zeng_saville_olarte_carbone_hu_seguin-orlando_samaniego_et al._2015, title={Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species}, volume={61}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/s00294-015-0480-3}, DOI={10.1007/s00294-015-0480-3}, abstractNote={Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.}, number={4}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Lassiter, Erica S. and Russ, Carsten and Nusbaum, Chad and Zeng, Qiandong and Saville, Amanda C. and Olarte, Rodrigo A. and Carbone, Ignazio and Hu, Chia-Hui and Seguin-Orlando, Andaine and Samaniego, Jose A. and et al.}, year={2015}, month={Mar}, pages={567–577} }
 @article{krings_saville_2007, title={Two new species and three lectotypifications in the Ibatia-Matelea complex (Apocynaceae : Asclepiadoideae) from northern South America}, volume={32}, ISSN={["1548-2324"]}, DOI={10.1600/036364407783390809}, number={4}, journal={SYSTEMATIC BOTANY}, author={Krings, Alexander and Saville, Amanda C.}, year={2007}, pages={862–871} }