Population Genomic Analysis of the Rice Blast Fungus Reveals Specific Events Associated With Expansion of Three Main Clades

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.

本研究对100株稻瘟病菌（Magnaporthe oryzae，曾用名Pyricularia oryzae，稻瘟病的致病菌）的基因组开展了分析。我们将当前田间稻瘟病菌种群划分为三个全球广泛分布的主要进化支类群。进化支1遗传多样性丰富，其可能代表一组亲缘关系紧密的演化支系，涵盖两种交配型的菌株。进化支2与进化支3为两个分化显著的类群，均起源自该高遗传多样性进化支的无性繁殖系谱，且与母支存在显著差异。对交配通路相关基因的分析显示，多个在其他真菌中存在交配行为相关直系同源基因的位点，呈现出进化支特异性的分化特征。每个无性繁殖系谱内的所有菌株均为同一交配型。我们经鉴定确认，某基因编码的小型富半胱氨酸蛋白为致病因子，而进化支2的标志性特征为该基因存在独特的缺失等位基因。进化支3的菌株在MFA2信息素前体基因区域存在小型缺失，且该缺失等位基因与我们划归至进化支1的一组特殊菌株共享，这类菌株携带AVR1-CO39等位基因。上述分子标记可用于菌株的快速筛选，同时也揭示了塑造该病菌种群结构的特定演化事件。本研究结果与现有学术观点一致：亚洲地区的稻瘟病菌种群通过基因重组产生遗传多样性，且该区域或为构成全球种群主体的进化支2与进化支3菌株的起源地。