Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae

文献类型： 外文期刊

第一作者： Bao, Jiandong

作者： Bao, Jiandong;Wang, Zhe;Chen, Shijie;Zheng, Huakun;Chen, Meilian;Wang, Zonghua;Chen, Xiaomin;Xie, Jiahui;Tang, Wei;Wang, Zonghua

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关键词： Pyricularia oryzae; pan-genome; rice blast; population structure; secreted proteins

期刊名称：JOURNAL OF FUNGI （ 影响因子：5.724； 五年影响因子：6.413 ）

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年卷期： 2022 年 8 卷 12 期

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收录情况： SCI

摘要： (1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pangenome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (similar to 70%) core genes (population frequency >= 95%) and 1378 (similar to 5%) strain-specific genes (population frequency <= 5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus.

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