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Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes
Author(s) -
Thilliez Gaetan J. A.,
Armstrong Miles R.,
Lim TzeYin,
Baker Katie,
Jouet Agathe,
Ward Ben,
Oosterhout Cock,
Jones Jonathan D. G.,
Huitema Edgar,
Birch Paul R. J.,
Hein Ingo
Publication year - 2019
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.15441
Subject(s) - phytophthora infestans , biology , oomycete , effector , virulence , population , genetics , pathogen , genome , genomics , phytophthora , gene , plant disease resistance , computational biology , botany , demography , sociology , microbiology and biotechnology
Summary 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 RXLR s 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.