Complete Genome Analysis of <i>Vibrio mimicus</i> strain SCCF01, a highly virulent isolate from the freshwater catfish

<i>Vibrio mimicus</i> is a foodborne pathogen, which is widely distributed in the aquatic environment. Moreover, it is often involved in aquatic animal diseases. In recent years, <i>V. mimicus</i> is an emerging pathogen in some species of Silurifomes. The strain SCCF01 was isolated from yellow catfish (<i>Pelteobagrus fulvidraco</i>). In this study, we aimed to perform genomic analysis of <i>V. mimicus</i> strain SCCF01 to identify genetic features and evolutionary relationships. Information on gene function and classification was obtained by functional annotation, and circular graph of strain SCCF01 genome, which was created by Circos v0.64. Information on virulence genes (adhesion, flagellum system, exotoxin and secretory system etc) was obtained by virulence genes annotation. Genome element prediction showed that most of the mobile elements were distributed in chromosome I. Therefore, chromosome I of SCCF01 genome has more plasticity than chromosome II and might be larger in size. Genomic linear relationship between the strain of <i>V. mimicu</i>s and strain SCCF01 was analyzed by linear pairwise comparison, but was unable to determine the relationship. Gene family analysis predicted that the evolutionary direction of strain SCCF01 was: clinical strain → environmental strain → SCCF01 strain. Phylogenetic analysis showed that the strain SCCF01 was more closely related to environmental strains. According to gene family analysis and phylogenetic analysis, we speculated that strain SCCF01 has probably diverged from environmental strains.

拟态弧菌（<i>Vibrio mimicus</i>）是一种食源性致病菌，广泛分布于水生环境中，且常引发水生动物病害。近年来，拟态弧菌成为部分鲶形目（Siluriformes）物种的新兴致病菌。菌株SCCF01分离自黄颡鱼（<i>Pelteobagrus fulvidraco</i>）。本研究旨在对拟态弧菌SCCF01菌株开展基因组分析，以解析其遗传特征与进化关系。通过功能注释获取基因功能与分类信息，并借助Circos v0.64绘制了SCCF01菌株的基因组环状图谱。通过毒力基因注释，获取了该菌株的毒力基因相关信息，包括黏附素、鞭毛系统、外毒素以及分泌系统等。基因组元件预测结果显示，绝大多数可移动元件均分布于一号染色体上。由此可见，SCCF01基因组的一号染色体相较于二号染色体具有更高的可塑性，且其尺寸可能更大。通过线性两两比对分析拟态弧菌其他菌株与SCCF01菌株的基因组线性关联特征，但未明确二者的关联关系。基因家族分析预测SCCF01菌株的进化路径为：临床菌株→环境菌株→SCCF01菌株。系统发育分析结果表明，SCCF01菌株与环境菌株的亲缘关系更为密切。综合基因家族分析与系统发育分析结果，本研究推测SCCF01菌株大概率由环境菌株演化而来。