College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.
Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
Microb Genom. 2020 Feb;6(2). doi: 10.1099/mgen.0.000322.
and are important fish pathogens affecting cultured and wild fish worldwide. To investigate the genome-level differences and similarities between catfish-adapted strains in these two species, the complete 93-146 and C07-087 genomes were evaluated by applying comparative genomics analysis. All available complete (10) and non-complete (19) genomes from five species were also included in a systematic analysis. Average nucleotide identity and core-genome phylogenetic tree analyses indicated that the five species were separated from each other. Pan-/core-genome analyses for the 29 strains from the five species showed that genus members have 9474 genes in their pan genome, while the core genome consists of 1421 genes. Orthology cluster analysis showed that and genomes have the greatest number of shared clusters. However, and also have unique features; for example, the genome encodes urease enzymes and cytochrome o ubiquinol oxidase subunits, whereas genomes encode tetrathionate reductase operons, capsular polysaccharide synthesis enzymes and vibrioferrin-related genes. Additionally, we report for what is believed to be the first time that 93-146 and three other genomes encode a type IV secretion system (T4SS), whereas none of the genomes encode this system. Additionally, the C07-087 genome encodes two different type VI secretion systems. genomes tend to encode more insertion elements, phage regions and genomic islands than . We speculate that the T4SS could contribute to the increased number of mobilome elements in compared to . Two of the genomes encode full CRISPR-Cas regions, whereas none of the genomes encode Cas proteins. Overall, comparison of the and genomes reveals unique features and provides new insights on pathogenicity that may reflect the host adaptation of the two species.
和 是影响全球养殖和野生鱼类的重要鱼类病原体。为了研究这两个物种中适应鲶鱼的菌株在基因组水平上的差异和相似性，通过比较基因组学分析评估了完整的 93-146 和 C07-087 基因组。还将来自五个 物种的所有可用完整（10 个）和非完整（19 个）基因组纳入系统分析。平均核苷酸同一性和核心基因组系统发育树分析表明，这五个 物种彼此分离。对来自五个物种的 29 个菌株的泛基因组/核心基因组分析表明，属成员在其泛基因组中有 9474 个基因，而核心基因组由 1421 个基因组成。同源聚类分析表明，和 基因组具有最多的共享聚类。然而，和 也有独特的特征；例如，基因组编码脲酶酶和细胞色素 o 泛醌氧化还原酶亚基，而 基因组编码四硫代盐还原酶操纵子、荚膜多糖合成酶和弧菌铁蛋白相关基因。此外，我们首次报道，93-146 和其他三个 基因组编码一种类型 IV 分泌系统（T4SS），而 基因组均不编码该系统。此外， 基因组 C07-087 编码两种不同的类型 VI 分泌系统。 基因组往往比 基因组编码更多的插入元件、噬菌体区和基因组岛。我们推测，T4SS 可能导致 比 具有更多的可移动元件。两个 基因组编码完整的 CRISPR-Cas 区，而 基因组均不编码 Cas 蛋白。总体而言，比较 和 基因组揭示了独特的特征，并提供了有关可能反映这两个物种宿主适应性的致病性的新见解。
