Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms. In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance. Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex.

中文翻译：

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对从患病海鱼半光滑舌鳎、半滑舌鲆中分离出的有毒圆弧菌 VSc190401 的全基因组分析

Vibrio scophthalmi是一种机会性细菌病原体，广泛分布于海洋环境中。早期的研究表明，它是大菱鲆肠道中的一种正常微生物。然而，最近的研究证实，这种细菌菌株可以在许多不同的海洋动物中引起疾病​​。因此，有必要对其全基因组进行研究，以更好地了解其生理和致病机制。在本研究中，我们从患病的半滑舌鳎（Cynoglossus semilaevis）中获得了一株 V. scophthalmi 的致病菌株，并对其全基因组进行了测序。它的基因组包含两条环状染色体和两个质粒，总大小为 3,541,838 bp，其中包含 3185 个编码基因。在这些基因中，通过COG、Blast2GO、和 KEGG 数据库。此外，通过IslandViewer在线系统预测染色体I中存在10个基因组岛。VFDB和PHI数据库中的比较分析表明，该菌株具有334个潜在毒力相关基因和518个病原体-宿主相互作用相关基因。虽然它含有与T1SS、T2SS、T4SS和T6SS四个分泌系统相关的基因，但只有一个完整的T2SS分泌系统。根据CARD数据库blast结果，在该菌株的全基因组中发现了属于27个抗生素抗性类别的180个耐药基因。然而，耐药性的表型和基因型之间存在许多差异。基于全基因组分析，致病性V. scophthalmi菌株含有多种与致病性和耐药性相关的基因。而且，在耐药性上表现出表型和基因型不一致。这些结果表明生理机制似乎很复杂。