title: Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing.
abstract: 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.
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Carly F
authors.initials: CF
authors.lastname: Summers
authors.affiliation: Cornell Laboratory for Accelerator-based Sciences and Education, Cornell University, Ithaca, New York, United States of America.
authors.forename: Colwyn M
authors.initials: CM
authors.lastname: Gulliford
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Craig H
authors.initials: CH
authors.lastname: Carlson
authors.affiliation: United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America.
authors.forename: Jacquelyn A
authors.initials: JA
authors.lastname: Lillis
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Maryn O
authors.initials: MO
authors.lastname: Carlson
authors.affiliation: United States Department of Agriculture Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, United States of America.
authors.forename: Lance
authors.initials: L
authors.lastname: Cadle-Davidson
authors.affiliation: United States Department of Agriculture Agricultural Research Service, Forage Seed and Cereal Research Unit and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: David H
authors.initials: DH
authors.lastname: Gent
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America.
authors.forename: Christine D
authors.initials: CD
authors.lastname: Smart
mesh_terms: D018553:Cucumis sativus; D014644:Genetic Variation / Q000235:genetics; D005838:Genotype; D044742:Peronospora / Q000472:pathogenicity*; D010935:Plant Diseases / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*