Table_2_Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level.XLSX

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

基因内的微卫星（Microsatellite）或称简单序列重复（Simple Sequence Repeat, SSR）不稳定现象可诱导遗传变异。作为最为成功的哺乳动物辐射演化类群之一，灵长总目（Euarchontoglires）内不同演化支的SSR特征仍鲜为人知。本研究对153个灵长总目物种的基因组开展了全基因组水平的跨分类学层级微卫星分布模式解析。结果显示，SSR的丰度与密度与灵长类基因组大小呈显著正相关，但未发现其与啮齿类基因组大小存在显著关联。此外，啮齿类的完美SSR（Perfect SSR, P-SSR）特征复杂度显著高于灵长类。在灵长类、树鼩与鼯猴的基因组中，单核苷酸型P-SSR为最常见的类型；而啮齿类与兔形目物种的基因组中，则以单核苷酸或二核苷酸基序类型占主导。具体而言，(A)n基序在灵长类基因组中丰度最高，而在啮齿类基因组中，(A)n、(AC)n或(AG)n为最丰基序，且同一属内的啮齿类物种间也存在差异。在不同分类学层级下，不同物种的P-SSR的GC含量与重复拷贝数存在差异，这反映了SSR突变过程的内在区别。值得注意的是，本研究通过基因本体（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）注释，对携带P-SSR的编码序列（Coding Sequence, CDS）进行了功能与通路分类，凸显了其在转录调控中的作用。总体而言，本研究将为后续解析灵长总目哺乳动物演化过程中微卫星分类学特征的功能角色提供助力。