Characterization of microsatellites in the endangered snow leopard based on the chromosome-level genome

The snow leopard ( Panthera uncia ) is an elusive high-altitude specialist and under substantial threat throughout its range. To characterize microsatellites (SSRs) for the snow leopard, we performed genome-mining and comparison of SSRs with 1–6 bp nucleotide motifs between the snow leopard and all other Panthera species. A total of 1,323,721 perfect SSRs were mined for the snow leopard, which is lower than the lion (1,346,471), leopard (1,527,334), and jaguar (1,508,527) but higher than the tiger (1,236,361). Mono-nucleotide SSRs were the most frequent perfect SSRs while hexa-nucleotide SSRs the least. The GC content was the highest in tri-nucleotide SSRs while the lowest in the mono-nucleotide SSRs. Location analysis revealed that microsatellites were predominantly concentrated at both ends of genes. Most genes containing microsatellite had the SSR present at only one locus, from which we infer that the number of SSRs per gene is limited even though intragenic tandem repeats can generate functional variability. Functional analysis of genes whose coding regions have SSRs identified items involved in metabolic process and immune system, which was possibly associated with high-altitude adaptation. SSR analysis can help to develop functional markers and facilitate further analysis of microsatellite function in the snow leopard. Our data and findings will be useful for understanding the frequency and the distribution of SSRs in the snow leopard genome and provide valuable resources for further development and identification of snow leopard SSRs, which facilitates the long-term conservation and genetic diversity for this endangered species.