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Article: Evaluation of a Formulation of

Hansel, Jeana / Saville, Amanda C / Ristaino, Jean Beagle

2024 Volume 108, Issue 4, Page(s) 1014–1024

Abstract: Phytophthora blight, caused ... ...

Abstract	Phytophthora blight, caused by
MeSH term(s)	Bacillus subtilis/drug effects ; Bacillus subtilis/physiology ; Phytophthora/drug effects ; Phytophthora/physiology ; Capsicum/microbiology ; Plant Diseases/prevention & control ; Plant Diseases/microbiology ; Pest Control, Biological/methods ; Biological Control Agents/pharmacology ; Fungicides, Industrial/pharmacology
Chemical Substances	Biological Control Agents ; Fungicides, Industrial
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-04-23-0807-RE
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in

Pais, Andrew / Ristaino, Jean / Whetten, Ross / Xiang, Qiu-Yun Jenny

Frontiers in plant science

2024 Volume 14, Page(s) 1282188

Abstract: Introduction: Understanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of ... ...

Abstract	Introduction: Understanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted. The flowering dogwood tree ( Methods: We conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of Results: Our data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues. Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses-suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity. Discussion: Our results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.
Language	English
Publishing date	2024-01-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2023.1282188
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A Lucid Key to the Common Species of Phytophthora.

Ristaino, Jean Beagle

Plant disease

2019 Volume 96, Issue 6, Page(s) 897–903

Abstract: The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 ... ...

Abstract	The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated "Fact Sheet" on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5' end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS-08-11-0636
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Article ; Online: Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents.

Saville, Amanda C / Ristaino, Jean B

Scientific reports

2021 Volume 11, Issue 1, Page(s) 12335

Abstract: The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex ... ...

Abstract	The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on six continents. The US-1 genotype was found later than FAM-1 on all continents except Australia/Oceania and in only 27% of the samples. FAM-1 was the first genotype detected in almost all the former British colonies from which samples were available. The data from historic outbreak samples suggest the FAM-1 genotype was widespread, diverse, and spread to Asia and Africa from European sources. The famine lineage spread to six continents over 144 years, remained widespread and likely spread during global colonization from Europe. In contrast, modern lineages of P. infestans are rapidly displaced and sexual recombination occurs in some regions.
MeSH term(s)	Evolution, Molecular ; Genotype ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; Phytophthora infestans/classification ; Phytophthora infestans/genetics ; Phytophthora infestans/pathogenicity ; Plant Diseases/microbiology ; Plant Diseases/statistics & numerical data ; Recombination, Genetic ; Solanum tuberosum/microbiology
Language	English
Publishing date	2021-06-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-90937-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Reconstructing historic and modern potato late blight outbreaks using text analytics.

Saffer, Ariel / Tateosian, Laura / Saville, Amanda C / Yang, Yi-Peng / Ristaino, Jean B

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2523

Abstract: In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the ... ...

Abstract	In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the disease should be managed. The pathogen, now known as Phytophthora infestans, still continues to threaten food security globally. A wealth of untapped knowledge exists in both archival and modern documents, but is not readily available because the details are hidden in descriptive text. In this work, we (1) used text analytics of unstructured historical reports (1843-1845) to map US late blight outbreaks; (2) characterized theories on the source of the pathogen and remedies for control; and (3) created modern late blight intensity maps using Twitter feeds. The disease spread from 5 to 17 states and provinces in the US and Canada between 1843 and 1845. Crop losses, Andean sources of the pathogen, possible causes and potential treatments were discussed. Modern disease discussion on Twitter included near-global coverage and local disease observations. Topic modeling revealed general disease information, published research, and outbreak locations. The tools described will help researchers explore and map unstructured text to track and visualize pandemics.
MeSH term(s)	Humans ; Phytophthora infestans ; Solanum tuberosum ; Plant Diseases ; Disease Outbreaks ; Ireland
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52870-2
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Article ; Online: An open-access T-BAS phylogeny for emerging Phytophthora species.

Coomber, Allison / Saville, Amanda / Carbone, Ignazio / Ristaino, Jean Beagle

PloS one

2023 Volume 18, Issue 4, Page(s) e0283540

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Phylogeny ; Phytophthora/genetics ; Genotype
Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0283540
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Article ; Online: Understanding the Genotypic and Phenotypic Structure and Impact of Climate on Phytophthora nicotianae Outbreaks on Potato and Tomato in the Eastern United States

Saville, Amanda C. / McGrath, Margaret T. / Jones, Chris / Polo, John / Ristaino, Jean Beagle

Phytopathology®. 2023 Aug., v. 113, no. 8 p.1506-1514

2023

Abstract: 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 ... ...

Abstract	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.
Keywords	Phytophthora infestans ; Phytophthora nicotianae ; climate ; climate change ; haplotypes ; heat tolerance ; inoculum ; mefenoxam ; microsatellite repeats ; phenotype ; potatoes ; tomatoes ; weather ; Maryland ; New York ; North Carolina ; Pennsylvania ; Virginia ; population genetics ; potato ; tomato
Language	English
Dates of publication	2023-08
Size	p. 1506-1514.
Publishing place	The American Phytopathological Society
Document type	Article ; Online
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-11-22-0411-R
Database	NAL-Catalogue (AGRICOLA)

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Article: Understanding the Genotypic and Phenotypic Structure and Impact of Climate on

Saville, Amanda C / McGrath, Margaret T / Jones, Chris / Polo, John / Ristaino, Jean B

Phytopathology

2023 Volume 113, Issue 8, Page(s) 1506–1514

Abstract: 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 ... ...

Abstract	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
Language	English
Publishing date	2023-10-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-11-22-0411-R
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Article: Genetic Structure and Subclonal Variation of Extant and Recent U.S. Lineages of

Saville, Amanda / Ristaino, Jean Beagle

Phytopathology

2019 Volume 109, Issue 9, Page(s) 1614–1627

Abstract: ... The ... ...

Abstract	The oomycete
MeSH term(s)	Brazil ; Genetic Structures ; Mexico ; Phytophthora infestans/physiology ; Plant Diseases/statistics & numerical data ; Solanum tuberosum ; United States
Language	English
Publishing date	2019-08-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-09-18-0357-R
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Ecologically Based Approaches to Management of Phytophthora Blight on Bell Pepper.

Ristaino, Jean Beagle / Johnston, Stephen A

Plant disease

2019 Volume 83, Issue 12, Page(s) 1080–1089

Language	English
Publishing date	2019-03-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS.1999.83.12.1080
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