Analysis of the distribution patterns and characteristics of microsatellites in <italic>Meles meles</italic> genome

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.