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

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...

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Bibliographic Details
Published in:PloS one 2015-11, Vol.10 (11), p.e0143665-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: Article
Language:English
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
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0143665