Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes

Thilliez, Gaetan J. A., Armstrong, Miles R., Lim, Tze-Yin, Baker, Katie, Jouet, Agathe, Ward, Ben, Van Oosterhout, Cock ORCID:, Jones, Jonathan D. G., Huitema, Edgar, Birch, Paul R. J. and Hein, Ingo (2019) Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytologist, 221 (3). pp. 1634-1648. ISSN 0028-646X

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The oomycete pathogens Phytophthora infestans and P. capsici cause significant crop losses world‐wide, threatening food security. In each case, pathogenicity factors, called RXLR effectors, contribute to virulence. Some RXLRs are perceived by resistance proteins to trigger host immunity, but our understanding of the demographic processes and adaptive evolution of pathogen virulence remains poor. Here, we describe PenSeq, a highly efficient enrichment sequencing approach for genes encoding pathogenicity determinants which, as shown for the infamous potato blight pathogen Phytophthora infestans, make up < 1% of the entire genome. PenSeq facilitates the characterization of allelic diversity in pathogen effectors, enabling evolutionary and population genomic analyses of Phytophthora species. Furthermore, PenSeq enables the massively parallel identification of presence/absence variations and sequence polymorphisms in key pathogen genes, which is a prerequisite for the efficient deployment of host resistance genes. PenSeq represents a cost‐effective alternative to whole‐genome sequencing and addresses crucial limitations of current plant pathogen population studies, which are often based on selectively neutral markers and consequently have limited utility in the analysis of adaptive evolution. The approach can be adapted to diverse microbes and pathogens.

Item Type: Article
Uncontrolled Keywords: penseq,phytophthora capsici,phytophthora infestans,rxlr effectors,avirulence,population genomics,virulence,physiology,plant science,sdg 2 - zero hunger ,/dk/atira/pure/subjectarea/asjc/1300/1314
Faculty \ School: Faculty of Science > School of Environmental Sciences
Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation
Faculty of Science > Research Groups > Plant Sciences
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Depositing User: LivePure Connector
Date Deposited: 22 Oct 2018 15:30
Last Modified: 22 Oct 2022 04:11
DOI: 10.1111/nph.15441


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