ArticleThe New phytologist2019
Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes.
Article in The New phytologist, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Population Genomics Reveals Distinct Lineage of the Asian Soybean Rust Fungus Phakopsora pachyrhizi in the United States of America Unrelated to Brazilian Populations.Molecular plant pathology · 2025Article
- Review
- Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation inEvolutionary applications · 2025Article
- Alternative splicing of a potato disease resistance gene maintains homeostasis between growth and immunity.The Plant cell · 2024Article
- Evolution of Phytophthora infestans on its potato host since the Irish potato famine.Nature communications · 2024Article
- Next-generation fungal identification using target enrichment and Nanopore sequencing.BMC genomics · 2023Article
- A single region of the Phytophthora infestans avirulence effector Avr3b functions in both cell death induction and plant immunity suppression.Molecular plant pathology · 2023Article
- How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?Plant molecular biology · 2022Review
- "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants?Virulence · 2021Article
- Multiple Mechanisms Drive the Evolutionary Adaptation ofJournal of fungi (Basel, Switzerland) · 2021Article
- Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae.Molecular plant pathology · 2021Article
- Quantitative resistance differences between and within natural populations ofEcology and evolution · 2021Article
- Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics.Plants (Basel, Switzerland) · 2021Review
- The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode,Genes · 2020Article
- Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq).Molecular plant pathology · 2020Article
- RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes.The New phytologist · 2020Article
- Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits.Plant pathology · 2020Review
- High-resolution expression profiling of selected gene sets during plant immune activation.Plant biotechnology journal · 2020Article
- A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.Frontiers in genetics · 2019Review
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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.
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