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

Gaëtan J. A. Thilliez, Miles Armstrong, Joanne Tze-Yin Lim, Katie Baker, Agathe Jouet, Ben Ward , Cock van Oosterhout, Jonathan D. G. Jones, Edgar Huitema, Paul Birch, Ingo Hein (Lead / Corresponding author)

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Abstract

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.

Original languageEnglish
Number of pages15
JournalNew Phytologist
Early online date5 Oct 2018
DOIs
Publication statusE-pub ahead of print - 5 Oct 2018

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Oomycetes
Metagenomics
Phytophthora infestans
Virulence
pathogens
Genome
Phytophthora
Genes
High-Throughput Nucleotide Sequencing
Food Supply
Virulence Factors
Solanum tuberosum
Immunity
Demography
Costs and Cost Analysis
virulence
pathogenicity
Population
food defense
Proteins

Keywords

  • PenSeq
  • Phytophthora capsici
  • Phytophthora infestans
  • RXLR effectors
  • avirulence
  • population genomics
  • virulence

Cite this

Thilliez, Gaëtan J. A. ; Armstrong, Miles ; Lim, Joanne Tze-Yin ; Baker, Katie ; Jouet, Agathe ; Ward , Ben ; Oosterhout, Cock van ; Jones, Jonathan D. G. ; Huitema, Edgar ; Birch, Paul ; Hein, Ingo. / Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. In: New Phytologist. 2018.
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Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. / Thilliez, Gaëtan J. A.; Armstrong, Miles; Lim, Joanne Tze-Yin; Baker, Katie; Jouet, Agathe ; Ward , Ben ; Oosterhout, Cock van ; Jones, Jonathan D. G.; Huitema, Edgar; Birch, Paul; Hein, Ingo (Lead / Corresponding author).

In: New Phytologist, 05.10.2018.

Research output: Contribution to journalArticle

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