Abstract:

The Eurasian badger (Meles meles) belongs to the order Carnivora and the genus Meles. It lives in social groups in underground environments and exhibits distinct territorial behaviors. The Eurasian badger is primarily nocturnal, with a broad dietary preference, and it is also an important wildlife host for bovine tuberculosis. This study systematically investigates the distribution characteristics of microsatellites in the Eurasian badger genome using bioinformatics methods and annotates and functionally analyzes genes containing microsatellites in coding regions. The results show that the Eurasian badger genome is 2.74 Gb in size and contains 975 935 microsatellites, with a relative abundance of 356.35 loci/Mb. The distribution pattern of microsatellites across the whole genome is as follows: mononucleotide > dinucleotide > tetranucleotide > trinucleotide > pentanucleotide > hexanucleotide repeats. Among these, dinucleotide repeats have the highest GC content, while mononucleotide repeats have the lowest. Microsatellites with A/T-rich sequences dominate in the genome. The abundance of microsatellites varies in different regions of the genome, with the highest number found in intergenic regions (595 769), the highest relative abundance in introns (385.22 loci/Mb), and the lowest in coding regions (1 724 loci and 48.40 loci/Mb). The distribution characteristics of microsatellites in intergenic regions are similar to those in the whole genome, while the exons show a higher frequency of trinucleotide repeats, with a strong preference for trinucleotide and hexanucleotide repeat types in the coding regions. Regarding the positional features of microsatellite abundance, the highest abundance is found in the intron regions, followed by the 500 bp upstream and downstream regions of genes, with the lowest in the exonic regions. There are 1 724 CDSs containing microsatellites in the Eurasian badger genome, with 1 325 genes annotated in the Gene Ontology (GO) database, which are assigned to 11 971 GO terms and categorized into 39 major functional groups. The most significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway is the signaling pathway, containing 207 genes. This study provides fundamental data for the subsequent development of high-quality microsatellite markers for the Eurasian badger and offers a reference for understanding the functional and distribution characteristics of microsatellites in the whole genome of carnivorous species.

Key words: Meles meles, Microsatellite, Distribution patterns, GO analysis, KEGG enrichment

摘要：

狗獾（Meles meles）隶属食肉目狗獾属，以社会群体生活在地下环境中，具有明显的领地行为。狗獾主要在夜间活动，具有广泛的食物偏好，同时也是牲畜结核病感染的重要野生动物宿主。本研究运用生物信息学手段对狗獾基因组微卫星的分布特征进行系统分析，并对编码区含有微卫星的基因进行注释和功能分析。结果表明，狗獾全基因组大小为2.74 Gb，含有975 935个微卫星，微卫星相对丰度为356.35 loci/Mb。全基因组微卫星分布模式为单碱基重复序列 > 二碱基重复序列 > 四碱基重复序列 > 三碱基重复序列 > 五碱基重复序列 > 六碱基重复序列，其中GC含量二碱基重复最高，单碱基重复最低，微卫星中富含A/T碱基的重复序列占据明显优势。狗獾微卫星在基因组不同区域丰度不同，其中基因间区数量最多（595 769个），内含子相对丰度最高（385.22 loci/Mb），编码区数量（1 724个）和丰度（48.40 loci/Mb）最小。基因间区与全基因组微卫星的分布特征相似，而外显子中三碱基重复类型较为丰富，其中编码区表现出对三碱基重复和六碱基重复类型的强烈偏好。对于微卫星丰度分布的位置特征，微卫星在内含子区域丰度最高，其次为基因上下游500 bp，外显子区域最低。狗獾基因组中含有微卫星的CDS有1 724条，GO注释到1 325个基因，分配到11 971个GO条目，并归类到39个主要基因功能中。KEGG富集最显著的通路为信号传导通路，含有207个基因。本研究结果为后续开发狗獾高质量微卫星标记提供基础数据，也为理解食肉目物种微卫星在全基因组中的功能及分布特点提供了参考。

关键词: 狗獾, 微卫星, 分布规律, GO分析, KEGG富集