Siddiqe Rasel, Ghosh Ajit
Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
Gene Rep. 2021 Jun;23:101020. doi: 10.1016/j.genrep.2021.101020. Epub 2021 Jan 26.
Simple sequence repeats (SSRs) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, the presence and incidence of SSR on viral genomes are less studied. With the emergence of novel infectious viruses over the past few decades, it is imperative to study the genetic diversity in such viruses to predict their evolutionary and functional changes over time. Following the emergence of SARS-CoV-2, we have assembled 121 complete genomes reported from 31 countries across the six continents for the identification and characterization of SSR repeats. Using two independent SSR identification tools, we have found remarkable consistency in the diversity of microsatellites pattern (38-42 per genome) found in the 121 analyzed SARS-CoV-2 genomes indication their important role for genome stability. Among the identified motifs, trinucleotide and hexanucleotide repeats were found to be the most abundant form followed by mono- and di-nucleotide. There were no tetra- or penta-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetics, evolutionary analysis, strain identification and genetic variation.
简单序列重复（SSRs），即微卫星，是在真核生物（植物）和原核生物（细菌）中得到广泛研究的短重复序列。与其他生物相比，病毒基因组中SSRs的存在和发生率的研究较少。在过去几十年中，随着新型传染性病毒的出现，研究此类病毒的遗传多样性以预测其随时间的进化和功能变化变得势在必行。在严重急性呼吸综合征冠状病毒2（SARS-CoV-2）出现后，我们收集了来自六大洲31个国家报告的121个完整基因组，用于识别和表征SSRs重复序列。使用两种独立的SSRs识别工具，我们发现在121个分析的SARS-CoV-2基因组中发现的微卫星模式多样性（每个基因组38 - 42个）具有显著一致性，表明它们对基因组稳定性具有重要作用。在鉴定出的基序中，三核苷酸和六核苷酸重复被发现是最丰富的形式，其次是单核苷酸和二核苷酸。在分析的SARS-CoV-2基因组中没有四核苷酸或五核苷酸重复。在SARS-CoV-2基因组中发现微卫星可能对群体遗传学、进化分析、菌株鉴定和遗传变异有用。
