Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, 824236, India.
Funct Integr Genomics. 2024 Nov 15;24(6):213. doi: 10.1007/s10142-024-01498-6.
Microsatellites, or simple sequence repeats (SSRs), are repetitive DNA sequences typically composed of 1-6 nucleotides. These repetitive sequences are found in almost all genomes, including chloroplasts and mitochondria, and are widely distributed throughout the genomes. Microsatellites are highly polymorphic, and their length may differ from species to species. Consequently, microsatellites are widely used as molecular markers and play pivotal roles in various biological research. However, comprehensive information about the length variation of microsatellites in various organellar genome sequences is not available. Therefore, to provide mined information and explore the variability in the length of microsatellites across species, we developed a comprehensive resource named pSATdb 2.0 (polymorphic microSATellites database; https://bioinfo.icgeb.res.in/psatdb/ ). This upgraded version of its predecessor pSATdb provides comprehensive information on the frequency and distribution of 348,894 microsatellites identified in organellar genome sequences. These sequences originate from 15,681 organisms spanning 3252 genera within Metazoa and Viridiplantae. Remarkably, pSATdb 2.0 is the only database that offers information on common and polymorphic microsatellites detected between organisms, along with unique microsatellites specific to each genus. Furthermore, this database features unrestricted access and includes pioneer functionalities such as Advanced Search, BLAST, and JBrowse, which facilitate user-specific microsatellite search and its visualization within the database. The pSATdb holds immense potential for the research community to support diverse studies, including genetic diversity, genetic mapping, marker-assisted selection, and comparative population investigations.
微卫星，或简单重复序列（SSR），是由 1-6 个核苷酸组成的重复 DNA 序列。这些重复序列存在于几乎所有的基因组中，包括叶绿体和线粒体，并且广泛分布于基因组中。微卫星高度多态性，其长度可能因物种而异。因此，微卫星被广泛用作分子标记，并在各种生物学研究中发挥关键作用。然而，关于各种细胞器基因组序列中微卫星长度变化的综合信息尚不可用。因此，为了提供挖掘的信息并探索物种间微卫星长度的可变性，我们开发了一个名为 pSATdb 2.0（多态性微卫星数据库；https://bioinfo.icgeb.res.in/psatdb/）的综合资源。该版本是其前身 pSATdb 的升级版，提供了在细胞器基因组序列中鉴定的 348,894 个微卫星的频率和分布的综合信息。这些序列来自 15,681 个生物体，跨越 3252 个门和绿藻门的属。值得注意的是，pSATdb 2.0 是唯一一个提供了在生物体之间检测到的常见和多态性微卫星以及每个属特有的独特微卫星的信息的数据库。此外，这个数据库具有无限制的访问权限，并包含了一些先驱性功能，如高级搜索、BLAST 和 JBrowse，这些功能有助于用户特定的微卫星搜索及其在数据库中的可视化。pSATdb 为研究社区提供了巨大的潜力，支持包括遗传多样性、遗传图谱、标记辅助选择和比较群体研究在内的多种研究。
