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Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex |
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| Authors: | Chad Fautt Kevin L. Hockett Estelle Couradeau |
| Affiliation: | 1. Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, USA;2. Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, USA Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania, USA;3. Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, Pennsylvania, USA |
| 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. |
| Keywords: | classification effector proteins PCR Pseudomonas syringae type III secretion system virulence factors |