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

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.

Suggested Citation

  • Carly F Summers & Colwyn M Gulliford & Craig H Carlson & Jacquelyn A Lillis & Maryn O Carlson & Lance Cadle-Davidson & David H Gent & Christine D Smart, 2015. "Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-19, November.
    • Handle: RePEc:plo:pone00:0143665
    DOI: 10.1371/journal.pone.0143665
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    1. Peristera Paschou & Elad Ziv & Esteban G Burchard & Shweta Choudhry & William Rodriguez-Cintron & Michael W Mahoney & Petros Drineas, 2007. "PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-15, September.
    2. Stephen C. Whisson & Petra C. Boevink & Lucy Moleleki & Anna O. Avrova & Juan G. Morales & Eleanor M. Gilroy & Miles R. Armstrong & Severine Grouffaud & Pieter van West & Sean Chapman & Ingo Hein & Ia, 2007. "A translocation signal for delivery of oomycete effector proteins into host plant cells," Nature, Nature, vol. 450(7166), pages 115-118, November.
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    1. Zachariah R Hansen & Kathryne L Everts & William E Fry & Amanda J Gevens & Niklaus J Grünwald & Beth K Gugino & Dennis A Johnson & Steven B Johnson & Howard S Judelson & Brian J Knaus & Margaret T McG, 2016. "Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology," PLOS ONE, Public Library of Science, vol. 11(11), pages 1-22, November.

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