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

Abstract

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 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.

High‐resolution expression profiling of selected gene sets during plant immune activation

“…In addition, ten times more multiplexed libraries than this study can be included in the same flow cell to achieve the same read depth and coverage compared to the conventional genome-wide RNA-seq for differential gene expression analysis. Finally, capture-seq could also be used to investigate expression of specific pathogen genes during host colonization (Pathogen Enrichment Sequencing: PenSeq) Thilliez et al, 2019). In summary, sequence capture provides an extremely versatile and cost-effective method to investigate changes in expression of any designated gene set.…”

“…Sequence capture can help generate high-resolution quantitative data sets to assess changes in abundance of selected genes. We previously used sequence capture to accelerate Resistance gene cloning (Jupe et al, 2013;Witek et al, 2016a, b), investigate immune receptor gene diversity (Van de Weyer et al, 2019) and investigate pathogen diversity and evolution Thilliez et al, 2019). The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors.…”

Albugo candida race diversity, ploidy and host‐associated microbes revealed using DNA sequence capture on diseased plants in the field

“…Potential applications would be to study the coevolution of host resistance genes and pathogen effectors in natural populations or of microorganisms within specific environments. Sequence capture has been used to sequence viral genomes from clinical samples (VirCapSeq; Briese et al ., ) and in a companion paper, PenSeq was used to investigate putative effector sequences in P. infestans and Phytophthora capsici (Thilliez et al ., ). Although field pathogenomics can also be very helpful for assigning races to lineages (Hubbard et al ., ), sequence capture enables the sequences under investigation to be predefined.…”

PenSeq: coverage you can count on

“…As Thilliez et al . point out, the known and putative pathogenicity determinants for P. infestans, and several other Phytophthora species, make up < 1% of the genome in terms of base pairs. Filtering out c .…”

“…While landmark population genetic studies have made instrumental contributions, the ability to simultaneously characterize a large number of genes with the same experimental rigor as used for a single locus, or a small subgroup of loci, has remained elusive. To address this challenge, Thilliez et al ., in this issue of New Phytologist (pp. 1634–1648), developed an elegant method, Pathogen Enrichment Sequencing (PenSeq), to conduct targeted population genetics studies for several Phytophthora species at an unprecedented sequencing depth using a substantial number of targeted genes.…”