@article{5e3cb82a06214224a3e141ab08347388,
title = "Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex",
abstract = "The Pseudomonas syringae species complex is composed of several closely related species of bacterial plant pathogens. Here, we used in silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluated their in silico amplification rate in 2161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity, and trained naive Bayes classification models to quantify classification resolution. Furthermore, we show the potential for using single amplicon sequence data to predict type III effector protein repertoires, which are important determinants of host specificity and range.",
author = "Chad Fautt and Hockett, {Kevin L.} and Estelle Couradeau",
note = "Funding Information: This material is based on work supported by the National Institute of Food and Agriculture, US Department of Agriculture, through the Northeast Sustainable Agriculture Research and Education Program under subaward number GNE20‐232. C.F. is supported by the College of Agricultural Sciences, Pennsylvania State University and the Department of Plant Pathology and Environmental Microbiology (Penn State) through the mBiome initiative. E.C. is supported by Hatch fund 4710 entitled Fates of Soil Carbon and Nitrogen in Agricultural Systems in the College of Agricultural Sciences (Penn State) and the Huck Institute for the Life Sciences (Penn State). The authors also acknowledge the Penn State Microbiome Center, a community of scholars and students who coordinate and accelerate interdisciplinary discovery and applications to establish long‐lasting resources in the field of microbiome research. Additional support for K.L.H. came from the USDA National Institute of Food and Agriculture and Federal Hatch Appropriations PEN04648 (accession no. 1016871) and start‐up funds through the Huck Institutes for the Life Sciences and the College of Agricultural Sciences, Pennsylvania State University. Funding Information: This material is based on work supported by the National Institute of Food and Agriculture, US Department of Agriculture, through the Northeast Sustainable Agriculture Research and Education Program under subaward number GNE20-232. C.F. is supported by the College of Agricultural Sciences, Pennsylvania State University and the Department of Plant Pathology and Environmental Microbiology (Penn State) through the mBiome initiative. E.C. is supported by Hatch fund 4710 entitled Fates of Soil Carbon and Nitrogen in Agricultural Systems in the College of Agricultural Sciences (Penn State) and the Huck Institute for the Life Sciences (Penn State). The authors also acknowledge the Penn State Microbiome Center, a community of scholars and students who coordinate and accelerate interdisciplinary discovery and applications to establish long-lasting resources in the field of microbiome research. Additional support for K.L.H. came from the USDA National Institute of Food and Agriculture and Federal Hatch Appropriations PEN04648 (accession no. 1016871) and start-up funds through the Huck Institutes for the Life Sciences and the College of Agricultural Sciences, Pennsylvania State University. Publisher Copyright: {\textcopyright} 2023 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.",
year = "2023",
month = aug,
doi = "10.1111/mpp.13337",
language = "English (US)",
volume = "24",
pages = "989--998",
journal = "Molecular plant pathology",
issn = "1464-6722",
publisher = "Wiley-Blackwell",
number = "8",
}