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

Abstract

Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversity and the consequences of host immunosuppression are poorly understood in the field.We report a method that enables sequencing of DNA of plant pathogens and plantassociated microbes directly from field samples (Pathogen Enrichment Sequencing: PenSeq). We apply this method to explore race diversity in A. candida and to detect A. candidaassociated microbes in the field (91 A. candida-infected plants).We show with unprecedented resolution that each host plant species supports colonization by one of 17 distinct phylogenetic lineages, each with an unique repertoire of effector candidate alleles. These data reveal the crucial role of sexual and asexual reproduction, polyploidy and host domestication in A. candida specialization on distinct plant species. Our bait design also enabled phylogenetic assignment of DNA sequences from bacteria and fungi from plants in the field. This paper shows that targeted sequencing has a great potential for the study of pathogen populations while they are colonizing their hosts. This method could be applied to other microbes, especially to those that cannot be cultured.

An evolutionary framework for host shifts – jumping ships for survival

“…This would lead to a reshuffling of effectors, which might lead to altered host ranges. This infrequent sexual reproduction by mostly clonal or selfing lineages can also explain the large host spectrum of Albugo candida as a species, while single genotypes have restricted host ranges (Thines, ; Jouet et al ., ). In powdery mildews, host shifts by effector re‐shuffling due to hybridisation have been observed (Menardo et al ., ), and in cases of overlapping hosts, hybrid‐driven host jumps may not be rare (Hacquard et al ., ; Thines, ; McMullan et al ., ; DePotter et al ., ).…”

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

“…Hence, we postulate that balancing selection, such as novel allele or rare allele advantage (Phillips et al ., ), is most consistent with the pattern of polymorphism at these seven PITG genes. In a companion paper, we show the population genetic application of PenSeq employed on field samples (Jouet et al ., ).…”

“…Biotinylated, RNA‐derived baits of 120 nucleotides (nt) in length were designed for targeted genes using end‐to‐end tilling and were manufactured by MY croarray (MYbaits; Ann Arbor, MI, USA). The library contains 18 348 baits in total (see Jouet et al ., ), 7296 of which were designed to target P. infestans and P. capsici genes. Of the latter, 3729 target P. infestans genes with gene identifiers (PITG, including predicted RXLRs and other genes of interest), 24 were specifically designed to enable the enrichment of additional RXLRs identified in the UK isolate 3928A, and 10 target other P. infestans genomic loci with no known PITG identifier.…”

PenSeq: coverage you can count on

“…Thilliez et al . and Jouet et al . both conducted a series of complementary experiments to realize and assess the practical values of PenSeq. Thilliez et al .'s portion of the enrichment library consisted of 7296 baits targeting the known and putative virulence factors (PITGs, RxLRs, CRNs, etc.)…”

“…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. Jouet et al . , also in this issue of New Phytologist (pp. 1529–1543), showcase the many strengths of PenSeq to gain novel insight into the race diversity of 91 Albugo candida isolates on infected plants largely throughout Europe.…”