Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat

Genomics Data Pub Date : 2017-09-01 DOI:10.1016/j.gdata.2017.06.006

Vishal Mevada , Shradhdha Patel , Jignesh Pandya , Himani Joshi , Rajesh Patel

{"title":"Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat","authors":"Vishal Mevada , Shradhdha Patel , Jignesh Pandya , Himani Joshi , Rajesh Patel","doi":"10.1016/j.gdata.2017.06.006","DOIUrl":null,"url":null,"abstract":"<div>Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204bp identified by with second largest size for Salinicoccus sp. reported in the NCBI genome database. A total of 652 degradative pathways were identified by KEGG map analysis. Comparative genomic analysis revealed Salinicoccus sp. BAB 3246 as most highly related to Salinicoccus halodurans H3B36. Data mining identified stress response genes and operator pathway for degradation of various environmental pollutants. Annotation data and analysis indicate potential use in pollution control in industrial influent and saline environment.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 30-34"},"PeriodicalIF":0.0000,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.06.006","citationCount":"6","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics Data","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2213596017301010","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 6

Abstract

Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp identified by with second largest size for Salinicoccus sp. reported in the NCBI genome database. A total of 652 degradative pathways were identified by KEGG map analysis. Comparative genomic analysis revealed Salinicoccus sp. BAB 3246 as most highly related to Salinicoccus halodurans H3B36. Data mining identified stress response genes and operator pathway for degradation of various environmental pollutants. Annotation data and analysis indicate potential use in pollution control in industrial influent and saline environment.

Abstract Image

查看原文本刊更多论文

古吉拉特邦沿海地区嗜盐盐球菌(Salinicoccus sp. bab3246)全基因组测序和注释

Salinicoccus sp. BAB 3246是从印度古吉拉特邦沿海地区地表水流中采集的海水样本中分离出的一种嗜盐细菌。经16sRNA测序，鉴定菌株为Salinicoccus sp. BAB 3246 (Genebank ID: KF889285)。本研究使用Ion Torrent PGM平台确定该生物的全基因组序列，然后使用CLC基因组工作台进行组装，并使用RAST、BASys和MaGe进行基因组注释。Salinicoccus sp.的全基因组序列为713,204 bp，在NCBI基因组数据库中排名第二。通过KEGG图谱分析，共鉴定出652条降解途径。对比基因组分析显示，Salinicoccus sp. BAB 3246与盐化盐球菌H3B36亲缘关系最密切。数据挖掘确定了各种环境污染物降解的应激反应基因和操作途径。注释数据和分析表明在工业进水和盐水环境的污染控制中具有潜在的用途。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genomics Data

自引率

0.00%

发文量

审稿时长

12 weeks