Abstract
We examined the genomes of 100 isolates of Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease. We grouped current field populations of M. oryzae into three major globally distributed groups. A genetically diverse group, clade 1, which may represent a group of closely related lineages, contains isolates of both mating types. Two well-separated clades, clades 2 and 3, appear to have arisen as clonal lineages distinct from the genetically diverse clade. Examination of genes involved in mating pathways identified clade-specific diversification of several genes with orthologs involved in mating behavior in other fungi. All isolates within each clonal lineage are of the same mating type. Clade 2 is distinguished by a unique deletion allele of a gene encoding a small cysteine-rich protein that we determined to be a virulence factor. Clade 3 isolates have a small deletion within the MFA2 pheromone precursor gene, and this allele is shared with an unusual group of isolates we placed within clade 1 that contain AVR1-CO39 alleles. These markers could be used for rapid screening of isolates and suggest specific events in evolution that shaped these populations. Our findings are consistent with the view that M. oryzae populations in Asia generate diversity through recombination and may have served as the source of the clades 2 and 3 isolates that comprise a large fraction of the global population.
Highlights
These authors contributed : Zhenhui Zhong, Meilian ChenData access: Sequencing raw reads and assembled contigs are available at NCBI under BioProject ID: PRJNA354675; BioSample: SAMN06050060–SAMN06050147; SRA: SRP132141.Electronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease, results in significant yield losses worldwide and is an important threat to food security [1, 2]
Consistent with phylogenomic result, both Principal component analysis (PCA) and STRUCTURE analysis categorized the isolates into three clades (Fig. 1b, c)
Our analysis revealed that M. oryzae populations diverged at about ~1000 years before present (YBP)
Summary
Understanding the structure of the current population and Forestry University, Fuzhou 350002, China 2 Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou 350002, China 3 Department of Plant Pathology and Microbiology, National. Relationships between populations adapted to different hosts have been defined using multiple gene loci and recently with population genomic analysis [16,17,18,19,20]. These studies are critical for understanding current population structures and the potential for invasion of new hosts, such as wheat [21]
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