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

• Published in: PloS one 2020-01, Vol.15 (1), p.e0221604-e0221604
• Main Authors: Arafa, Ramadan A, Kamel, Said M, Rakha, Mohamed T, Soliman, Nour Elden K, Moussa, Olfat M, Shirasawa, Kenta
• Format: Article
• Language: English
• Subjects: Agricultural research; Analysis; Asexual reproduction; Biology and Life Sciences; Blight; Breeding; Chromosomes; Cluster analysis; Computer and Information Sciences; Cultivars; Deoxyribonucleic acid; Disease control; Divergence; DNA; DNA sequencing; DNA, Mitochondrial - genetics; Egypt; Epidemics; Famine; Famines; Fungicides; Fungicides, Industrial - pharmacology; Gene sequencing; Genes; Genes, Mating Type, Fungal - genetics; Genetic polymorphisms; Genetic research; Genetic variability; Genomes; Genomics; Genotype; Genotyping; High-Throughput Nucleotide Sequencing; Ireland; Japan; Late blight; Lycopersicon esculentum - microbiology; Mating; Microsatellite Repeats - genetics; Mitochondria; Mitochondrial DNA; Next-generation sequencing; Nucleotide sequence; Nucleotides; Pathogens; People and Places; Phytophthora infestans; Phytophthora infestans - genetics; Phytophthora infestans - growth & development; Plant breeding; Plant diseases; Plant Diseases - genetics; Plant Diseases - microbiology; Plant pathology; Polymorphism; Population genetics; Potatoes; R&D; Reproduction (biology); Research & development; Research and Analysis Methods; Sequence Analysis, DNA; Simple sequence repeats; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Solanum tuberosum - microbiology; Technology; Tomatoes
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0221604

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.