Genomic divergence betweenDickeya zeaestrain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain

文献类型： 外文期刊

第一作者： Zhang, Jingxin

作者： Zhang, Jingxin;Shen, Huifang;Sun, Dayuan;Pu, Xiaoming;Yang, Qiyun;Lin, Birun;Arif, Mohammad;Hu, John

作者机构：

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2020 年 15 卷 10 期

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收录情况： SCI

摘要： Rice foot rot caused byDickeya zeaeis an important bacterial disease of rice worldwide. In this study, we identified a new strain EC2 from rice in Guangdong province, China. This strain differed from the previously identified strain from rice in its biochemical characteristics, pathogenicity, and genomic constituents. To explore genomic discrepancies between EC2 and previously identified strains from rice, a complete genome sequence of EC2 was obtained and used for comparative genomic analyses. The complete genome sequence of EC2 is 4,575,125 bp in length. EC2 was phylogenetically closest to previously identifiedDickeyastrains from rice, but not within their subgroup. In terms of secretion systems, genomic comparisons revealed that EC2 harbored only type I (T1SS), typeII (T2SS), and type VI (T6SS) secretion systems. The flagella cluster of this strain possessed specific genomic characteristics like otherD.zeaestrains from Guangdong and from rice; within this locus, the genetic diversity among strains from rice was much lower than that of within strains from non-rice hosts. Unlike other strains from rice, EC2 lost the zeamine cluster, but retained the clustered regularly interspaced short palindromic repeats-1 (CRISPR-1) array. Compared to the otherD.zeaestrains containing both exopolysaccharide (EPS) and capsular polysaccharide (CPS) clusters, EC2 harbored only the CPS cluster, while the other strains from rice carried only the EPS cluster. Furthermore, we found strain MS1 from banana, carrying both EPS and CPS clusters, produced significantly more EPS than the strains from rice, and exhibited different biofilm-associated phenotypes. Comparative genomics analyses suggest EC2 likely evolved through a pathway different from the otherD.zeaestrains from rice, producing a new type of rice foot rot pathogen. These findings emphasize the emergence of a new type ofD.zeaestrain causing rice foot rot, an essential step in the early prevention of this rice bacterial disease.

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