Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade

Huei-Mien Ke, Anuphap Prachumwat, Chun-Ping Yu, Yi-Ting Yang, Sutitcha Promsri, Kuan-Fu Liu, Chu-Fang Lo, Mei-Yeh Jade Lu, Mei-Chin Lai, Isheng J. Tsai, Wen-Hsiung Li
2017 Scientific Reports  
The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the
more » ... Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity. The genus Vibrio is a bacterial group widely distributed in the marine environment. The core of the Vibrio Harveyi clade consist of V. harveyi and its closely related species V. campbellii, V. owensii, V. jasicida and V. rotiferianus 1-3 , all of which are well recognized aquatic animal pathogens 4-10 . Their members are commonly used as models to study bacterial luminescence 11-13 , quorum sensing 14 , biofilm formation, multi-chromosomal genome organization 15,16 , and recombination patterns 2 . Their genetic and phenotypic signatures are highly similar; conventional biochemical tests and 16 S rDNA sequencing frequently led to species misidentifications in this clade 17,18 . A well-known example is the misclassification of V. campbellii as V. harveyi -while the two species share only 61-74% DNA sequence similarity, the similarity in their 16 S rDNA sequences is over 97% 1,17 . Consequently, multi-locus sequence analysis (MLSA) was later used for species classification 1,18-20 . Given the sequence of two concatenated house-keeping gene sets (ftsZ, mreB and topA, or rpoD, rctB and toxR), the Harveyi clade ATCC BAA-1116 and HY01 were found to be V. campbellii rather than V. harveyi 18 . The advent of next-generation sequencing has enabled multiple genome sequencing and assembly of Vibrio species. Such data have aided the study of phylogenomics 2,3,21 and the identification of diagnostic features in Vibrio species 22 . A recent study of V. harveyi compared the genome of this species with those of three other
doi:10.1038/srep41394 pmid:28145490 pmcid:PMC5286417 fatcat:wr5n4e5auzf5nb3o2gxvjra55m