Rediscovery and analysis of Phytophthora carbohydrate esterase (CE) genes revealing their evolutionary diversity

文献类型： 外文期刊

第一作者： Qian Kun

作者： Qian Kun;Li Deng-hui;Lin Run-mao;Shi Qian-qian;Mao Zhen-chuan;Yang Yu-hong;Feng Dong-xin;Xie Bing-yan;Lin Run-mao;Xie Bing-yan

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关键词： Phytophthora; carbohydrate esterase gene prediction; comparative genomic analysis; evolution; diversity

期刊名称：JOURNAL OF INTEGRATIVE AGRICULTURE （ 影响因子：2.848； 五年影响因子：2.979 ）

ISSN： 2095-3119

年卷期： 2018 年 17 卷 4 期

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收录情况： SCI

摘要： A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase (CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.

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