Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing

• Published in: PloS one Vol. 10; no. 11; p. e0143665
• Main Authors: Summers, Carly F, Gulliford, Colwyn M, Carlson, Craig H, Lillis, Jacquelyn A, Carlson, Maryn O, Cadle-Davidson, Lance, Gent, David H, Smart, Christine D
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.11.2015; Public Library of Science (PLoS)
• Subjects: Agriculture; Airborne microorganisms; Bioinformatics; Biology; Cucumis sativus; Deoxyribonucleic acid; DNA; DNA methylation; Downy mildew; Gene sequencing; Genes; Genetic diversity; Genetic Variation - genetics; Genetics; Genomes; Genomics; Genotype; Genotyping; Host specificity; Morphology; Ontology; Pathogenicity; Pathogens; Peronospora - pathogenicity; Phylogenetics; Plant Diseases - microbiology; Plant pathology; Plant sciences; Polymorphism; Polymorphism, Single Nucleotide - genetics; Principal components analysis; Pseudoperonospora cubensis; Pseudoperonospora humuli; Ribonucleic acid; RNA; Sequence Analysis, RNA - methods; Single-nucleotide polymorphism; Studies; Oregon; New York; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0143665

RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data set showed genetic separation between the two species. Additionally, results supported previous findings that P. cubensis isolates from squash are genetically distinct from cucumber and cantaloupe isolates. A PCA-based procedure was used to identify SNPs correlated with the separation of the two species, with 994 and 4,231 PCA-correlated SNPs found within the RNA-seq and GBS data, respectively. The corresponding unigenes (n = 800) containing these potential species-specific SNPs were then annotated and 135 putative pathogenicity genes, including 3 effectors, were identified. The characterization of genes containing SNPs differentiating these two closely related downy mildew species may contribute to the development of improved detection and diagnosis strategies and improve our understanding of host specificity pathways.