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Insights on genomic diversity of Vibrio spp. through Pan-genome analysis
Annals of Microbiology ( IF 3.0 ) Pub Date : 2019-12-07 , DOI: 10.1007/s13213-019-01539-7
Suganya Nathamuni , Ashok Kumar Jangam , Vinaya Kumar Katneni , Ashok Selvaraj , Karthic Krishnan , Sujeet Kumar , Satheesha Avunje , Sivamani Balasubramaniam , Monendra Grover , Shankar V. Alavandi , Vijayan K. Koyadan

The aquaculture sector is a major contributor to the economic and nutritional security for a number of countries. India’s total seafood exports for the year 2017–2018 accounted for US$ Million 7082. One of the major setbacks in this sector is the frequent outbreaks of diseases often due to bacterial pathogens. Vibriosis is one of the major diseases caused by bacteria of Vibrio spp., causing significant economic loss to the aquaculture sector. The objective of this study was to understand the genetic composition of Vibrio spp. Thirty-five complete genomes were downloaded from GenBank comprising seven vibrio species, namely, Vibrio alginolyticus, V. anguillarum, V. campbellii, V. harveyi, V. furnissii, V. parahaemolyticus, and V. vulnificus. Pan-genome analysis was carried out with coding sequences (CDS) generated from all the Vibrio genomes. In addition, genomes were mined for genes coding for toxin-antitoxin systems, antibiotic resistance, genomic islands, and virulence factors. Results revealed an open pan-genome comprising of 2004 core, 8249 accessory, and 6780 unique genes. Downstream analysis of genomes and the identified unique genes resulted in 312 antibiotic resistance genes, 430 genes coding for toxin and antitoxin systems along with 4802, and 4825 putative virulent genes from genomic island regions and unique gene sets, respectively. Pan-genome and other downstream analytical procedures followed in this study have the potential to predict strain-specific genes and their association with habitat and pathogenicity.

中文翻译:

关于弧菌属物种基因组多样性的见解。通过全基因组分析

水产养殖部门是许多国家经济和营养安全的主要贡献者。印度2017-2018年海产品出口总额为7082万美元。这一部门的主要挫折之一是经常由于细菌病原体引起的疾病频繁爆发。弧菌病是由弧菌属细菌引起的主要疾病之一,给水产养殖业造成了巨大的经济损失。这项研究的目的是了解弧菌的遗传组成。从GenBank下载了35个完整基因组,其包含七个弧菌种,即溶藻弧菌,鳗弧菌,坎贝尔弧菌,哈氏弧菌,弗氏弧菌,副溶血弧菌和创伤弧菌。使用从所有弧菌基因组产生的编码序列(CDS)进行泛基因组分析。此外,还从基因组中提取了编码毒素-抗毒素系统,抗生素抗性,基因组岛和毒力因子的基因。结果揭示了一个开放的全基因组,该基因组由2004个核心,8249个辅助基因和6780个独特基因组成。基因组和鉴定出的独特基因的下游分析产生了312种抗生素抗性基因,430种编码毒素和抗毒素系统的基因,以及分别来自基因组岛区域和独特基因组的4802和4825个推定有毒力基因。这项研究中采用的全基因组和其他下游分析程序有可能预测菌株特异性基因及其与生境和致病性的关联。结果揭示了一个开放的全基因组,该基因组由2004个核心,8249个辅助基因和6780个独特基因组成。基因组和鉴定出的独特基因的下游分析产生了312种抗生素抗性基因,430种编码毒素和抗毒素系统的基因,以及分别来自基因组岛区域和独特基因组的4802和4825个推定有毒力基因。这项研究中采用的全基因组和其他下游分析程序有可能预测菌株特异性基因及其与生境和致病性的关联。结果揭示了一个开放的全基因组,该基因组由2004个核心,8249个辅助基因和6780个独特基因组成。基因组和鉴定出的独特基因的下游分析产生了312种抗生素抗性基因,430种编码毒素和抗毒素系统的基因,以及分别来自基因组岛区域和独特基因组的4802和4825个推定有毒力基因。这项研究中采用的全基因组和其他下游分析程序有可能预测菌株特异性基因及其与生境和致病性的关联。分别来自基因组岛区域和独特基因组的4825个推定有毒基因。这项研究中采用的全基因组和其他下游分析程序有可能预测菌株特异性基因及其与生境和致病性的关联。分别来自基因组岛区域和独特基因组的4825个推定有毒基因。这项研究中采用的全基因组和其他下游分析程序有可能预测菌株特异性基因及其与生境和致病性的关联。
更新日期:2020-04-18
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