Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies

Abstract

Phytophthora infestans (Mont.) de Bary, a hemibiotrophic oomycete, has caused severe epidemics of late blight in tomato and potato crops around the world since the Irish Potato Famine in the 1840s. Breeding of late blight resistant cultivars is one of the most effective strategies to overcome this disruptive disease. However, P. infestans is able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability among P. infestans isolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence of P. infestans isolates. In this study, we analyzed the genomes of P. infestans isolates collected from Egypt and Japan using various molecular approaches including the mating type assay and genotyping simple sequence repeats, mitochondria DNA, and effector genes. We also analyzed genome-wide single nucleotide polymorphisms using double-digest restriction-site associated DNA sequencing and whole genome resequencing (WGRS). The isolates were classified adequately using high-resolution genome-wide approaches. Moreover, these analyses revealed new clusters of P. infestans isolates in the Egyptian population. Monitoring the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.

Fig 1. Clustering analysis of Phytophthora infestans isolates collected from Egypt and Japan using double-digest restriction-site associated DNA sequencing (ddRAD-Seq) data.

Clusters (EGY1-1, EGY1-2, EGY2, JPN1, and JPN2) are indicated with solid bars. Clusters determined using simple sequence repeats (SSRs), effector genes, mitochondrial DNA (mtDNA) polymorphisms, and mating types are shown as colored charts; same colors indicate the members of the same clusters. Isolates indicated in bold were used to perform whole genome resequencing (WGRS) analysis.

Fig 2. Principal component analysis (PCA) of P. infestans isolates.

Different colors indicate the five clusters, EGY1-1, EGY1-2, EGY2, JPN1, and JPN2, identified by clustering analysis.

Fig 3. WGRS-based clusters of P. infestans isolates.

P. infestans isolates sequenced in this study are indicated in bold. The remaining isolates represent those whose genome sequences were publicly available.