Yao Dan, Cheng Lei, Du Lianming, Li Meijin, Daroch Maurycy, Tang Jie
Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China.
Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China.
Life (Basel). 2021 Nov 18;11(11):1258. doi: 10.3390/life11111258.
Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of -like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size ( < 0.01) and negatively correlated with GC content ( < 0.05). Moreover, the motif (A/C) and (AG) was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of -like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of strains to globally diverse niches.
微卫星（简单序列重复，SSRs）广泛分布于几乎所有已知基因组中。在此，首次开展的一项研究旨在检测类菌株基因组中的微卫星和复合微卫星（CSSRs）。结果揭示了微卫星和复合微卫星在基因组中的分布、丰度、密度及多样性的多样模式，表明它们可能经历快速的进化变化。微卫星和复合微卫星的数量在基因组间分布极不均衡，分别从11,086至24,000以及从580至1865不等。在31个基因组中，二核苷酸微卫星是最丰富的类别，而在另外15个基因组中则呈现以下模式：单核苷酸微卫星 > 二核苷酸微卫星 > 三核苷酸微卫星。与微卫星和复合微卫星相关的模式在系统发育组间存在差异。微卫星和复合微卫星绝大多数分布于编码区。微卫星和复合微卫星的数量与基因组大小显著正相关（< 0.01），与GC含量负相关（< 0.05）。此外，单核苷酸和二核苷酸微卫星中（A/C）和（AG）基序占主导，并且在39个基因组中鉴定出了复合微卫星的独特基序。本研究首次深入探究了类菌株基因组中的微卫星和复合微卫星，将有助于了解它们的分布、预测其功能并追踪其进化。此外，所鉴定出的微卫星可能提供快速适应环境变化的进化优势，并且可能在菌株向全球不同生态位的世界性分布中发挥重要作用。
