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

Summers, Carly F.; Gulliford, Colwyn M.; Carlson, Craig H.; Lillis, Jacquelyn A.; Carlson, Maryn O.; Cadle-Davidson, Lance; Gent, David H.; Smart, Christine D.

Citeable URL: https://ir.library.oregonstate.edu/concern/articles/6t053h86r

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Creator	Summers, Carly F. Gulliford, Colwyn M. Carlson, Craig H. Lillis, Jacquelyn A. Carlson, Maryn O. Cadle-Davidson, Lance Gent, David H. Smart, Christine D.
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.
License	CC0 1.0 Universal
Resource Type	Article
DOI	https://doi.org/10.1371/journal.pone.0143665
Fecha Disponible	2016-01-07T20:43:43+00:00
Fecha de Emisión	2015-11-23
Citation	Summers, C. F., Gulliford, C. M., Carlson, C. H., Lillis, J. A., Carlson, M. O., Cadle-Davidson, L., ... & Smart, C. D. (2015). Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PLoS ONE, 10(11), e0143665. doi:10.1371/journal.pone.0143665
Journal Title	PLoS ONE
Journal Volume	10
Journal Issue/Number	11
Academic Affiliation	Botany and Plant Pathology
Declaración de derechos	No Copyright - United States
Related Items	Supporting information is available online:
Funding Statement (additional comments about funding)	Funding for this work was provided through the United States Department of Agriculture Organic Research and Extension Initiative (http://nifa.usda.gov/funding-opportunity/organic-agriculture-research-and-extension-initiative; NIFA contract no. 2012-51300-20006) and National Institutes of Health (http://www.nih.gov/; grant 1S10OD010693-01). Funding for C.F. Summers was also provided through an NSF Graduate Research Fellowship (www.nsfgrfp.org; DGE-1144153).
Publisher	Public Library of Science
Peer Reviewed	Yes
Language	English [eng]
Replaces	http://hdl.handle.net/1957/58029

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

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

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