Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
Gene. 2020 Oct 5;757:144919. doi: 10.1016/j.gene.2020.144919. Epub 2020 Jun 27.
Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.
简单序列重复（SSRs）是遗传变异的重要来源，为生物适应不同环境提供了基础。本研究检测了 29 种甲虫基因组中 SSR 的分布模式，并对含有完美 SSR（P-SSR）的 CDS 进行了基因本体论（GO）分析。结果表明，不完美 SSR（I-SSR）是甲虫基因组中最丰富的 SSR 类别，且在不同的基因组区域（CDS、exon 和 intron 区域）中均有分布。P-SSR、I-SSR、复合 SSR 和可变数串联重复的数量与甲虫基因组大小呈正相关，而 SSR 的频率和密度与基因组大小均不相关。此外，我们的研究结果表明，鞘翅目同一亚目或科内 P-SSR 的常见基因组特征很少。单核苷酸、二核苷酸、三核苷酸或四核苷酸 SSR 是甲虫基因组中最丰富的 P-SSR 类别。在甲虫基因组中单核苷酸 P-SSR 中最丰富的重复基元是（A）n，但其他长度类别最常见的重复基元在这些基因组中差异很大。此外，P-SSR 类型的 GC 含量在甲虫基因组和不同的基因组区域中存在差异。CV（变异系数）分析表明，P-SSR 重复拷贝数在 intron 中的变异比在 CDS 和 exon 中更高。含有 P-SSR 的 CDS 的 GO 术语主要富集在“结合”和“转录”等分子功能上。我们的研究结果将有助于研究微卫星异质性在甲虫适应中的功能作用。
