Comparative genomics of the fish pathogens 93-146 and C07-087.

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.