Nagpure Naresh Sahebrao, Rashid Iliyas, Pathak Ajey Kumar, Singh Mahender, Pati Rameshwar, Singh Shri Prakash, Sarkar Uttam Kumar
Division of Molecular Biology and Biotechnology, National Bureau of Fish Genetic Resources, Lucknow-226002, India.
Division of Fish Taxonomy and Resources, National Bureau of Fish Genetic Resources, Lucknow-226002, India.
PLoS One. 2015 Aug 28;10(8):e0136711. doi: 10.1371/journal.pone.0136711. eCollection 2015.
Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.
线粒体基因组序列已被广泛用于进化和系统发育研究。在脊椎动物中，鱼类是一个重要且多样的群体，其线粒体基因组序列在公共数据库中迅速增加。为了便于线粒体基因组分析并探索有价值的遗传信息，我们开发了鱼类线粒体基因组资源（FMiR）数据库，以提供一个用于线粒体基因组注释、物种鉴定和微卫星标记挖掘的工作平台。微卫星也被称为简单序列重复（SSR），并在群体遗传学、基因复制和标记辅助选择研究中用作分子标记。在这里，已经实现了易于使用的工具来挖掘SSR并设计引物以鉴定物种/栖息地特异性标记。此外，FMiR可以分析完整或部分线粒体基因组序列以鉴定物种并推断跨物种序列之间的亲缘距离。该数据库目前包含来自297个科和47个目的1302种鱼类的经过整理的线粒体基因组，这些鱼类来自咸水和淡水生态系统。此外，该数据库涵盖了从鱼类数据库（FishBase）和世界自然保护联盟红色名录（IUCN Red List）数据库下载的鱼类信息，如保护状况、生态系统、科、分布和出现情况。这些鱼类信息已被用于浏览属于特定类别的物种的线粒体基因组信息。该数据库在内容和纳入其他分析模块方面具有可扩展性。FMiR在Linux操作平台上运行，可通过URL http://mail.nbfgr.res.in/fmir在高性能服务器上访问。
