脊椎动物基因组含有丰富的微卫星信息。本研究对翼手目动物中的大蹄蝠全基因组及其基因的微卫星分布特征进行分析，并对含有微卫星编码序列的基因进行注释分析。结果表明，大蹄蝠全基因组大小为2.24 Gb，共含有497 883个微卫星，其中，数量和比例最多的是单碱基和二碱基重复类型，分别有173 953个 (34.94%) 和222 591个 (44.71%)，相对丰度分别为77.78 loci/Mb和99.52 loci/Mb。微卫星数量从单碱基重复到六碱基重复单元最多的类型分别为 (A)_n、(AC)_n、(TAT)_n、(TTTA)_n、(AACAA)_n和 (TATCTA)_n，比例分别为95.14%、55.25%、38.41%、22.17%、48.68%和20.30%。不同基因区和基因间区的数量及丰度不同，其中基因间区的微卫星数量及其丰度最大，分别为322 666 个和2 541.57 loci/Mb，编码区的微卫星数量及其丰度最小，分别为1 461个和461.98 loci/Mb。基因间区和全基因组的微卫星的分布特征相似。编码区最多的微卫星类型为三碱基重复单元，外显子最多的微卫星类型为单碱基、二碱基和三碱基重复单元。在微卫星丰度分布的位置特征分析中，基因上游500 bp、外显子、内含子和基因下游500 bp各个区域微卫星丰度分别为16 400.94 loci/Mb、972.12 loci/Mb、2 180.66 loci/Mb和3 899.89 loci/Mb。大蹄蝠基因中含有微卫星的编码序列 (Coding sequence, CDS) 1 461条，被注释到的基因有1 226个。GO注释到63个主要功能基因中，并分配到26 439个GO条目。KEGG富集最显著的是信号传导通路，含有146个基因。本研究结果不仅为大蹄蝠高质量微卫星的筛选提供参考，还将进一步为翼手目其他物种的全基因组微卫星分布特征分析及其微卫星在全基因组中的生物学功能研究提供参考。

The vertebrate genome is rich in microsatellite information. In this study, the distribution of microsatellite (SSRs) in the complete genome and its genes of Hipposideros armiger (Chiroptera) was analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) containing microsatellite coding sequence (CDS) were explored. The results showed that the total genome size of H. armiger was 2.24 Gb and contained 497 883 microsatellites. Mononucleotide (173 953 microsatellites) and dinucleotide repeats (222 591 microsatellites) were the most diverse in the genome of H. armiger accounting for 34.94% and 44.71% of whole genome size, with their relative abundance of 77.78 loci/Mb and 99.52 loci/Mb, respectively. The most microsatellite types from mononucleotide repeat to hexanucleotide repeat were (A)_n, (AC)_n, (TAT)_n, (TTTA)_n, (AACAA)_n and (TATATA)_n, with their frequency of 95.14%, 55.25%, 38.41%, 22.17%, 48.68% and 20.30% respectively. The number and abundance of microsatellites were different in both gene regions and intergenic regions. The diversity of microsatellites was highest in intergenic region with 322 666 microsatellites, and its abundance was 2 541.57 loci/Mb, whereas lowest in coding region with 1 461 microsatellites, and its abundance was 461.98 loci/Mb. The distribution characteristics of microsatellites in intergenic region and total genome were similar. Trinucleotide repeat were the most common types of microsatellites in the coding region, while mono-, di- and tri-nucleotide repeat were the most common types of microsatellites in the exons. The positional specificity of microsatellites abundance distributions in 500 bp upstream, exon, intron and 500 bp downstream were 16 400.94 loci/Mb, 972.12 loci/Mb, 2 180.66 loci/Mb and 3 899.89 loci/Mb, respectively. A total of 1 461 microsatellite coding sequences (CDS) were found in the genome of H. armiger, and 1 226 genes were annotated. GO was mainly annotated into 63 functional genes and assigned to 26 439 GO items. The most significant KEGG enrichment was in the signal transduction pathway, which contained 146 genes. The results of this study not only provide a reference for the screening of high-quality microsatellites in H. armiger, it will also provide a reference for genome-wide analysis of microsatellite distribution in other Chiroptera species and the study of their biological functions in the whole genome.