Distinct patterns of microsatellite and functional analysis of forest musk deer and its closely related species
Received date: 2021-12-01
Accepted date: 2022-07-05
Online published: 2022-12-02
Muscidae and Cervidae belong to artiodactyl ruminants and have important economic value. There is still a lack of relevant studies on using simple sequence repeats (SSRs) to reveal the phylogenetic relationship among species at the genomic level and to explore the gene functions of SSRs and their enriched signaling pathways. With the completion of the genome sequence of the forest musk deer (Moschus berezovskii), Siberian musk deer (Moschus moschiferus), the red deer (Cervus elaphus), the Reeves’ muntjac (Muntiacus reevesi), and the red muntjac (Muntiacus vaginalis), we extracted the coding sequences (CDS) of these species by bioinformatics method and analyzed the distribution patterns of coding SSR and their biological functions. The containing-SSR genes were enriched in the signal pathways and their association with disease were explored. The results prove that the proportion of their coding SSRs were 6.96% (1 696), 7.18% (2 359), 7.29% (3 005), 7.36% (1 916), and 7.48% (1 924), respectively. In addition, the distribution pattern of coding SSRs of the five species was similar, triplet repeats SSR (Tri- and Hexa-SSRs) of the five species were the most similar, which were 96.85%, 94.87%, 65.44%, 64.23%, and 88.04%, respectively. The GO functional enrichment showed that the SSR sequences in the CDS of the five species had many same enriched functions in three aspects: molecular function, cellular component, and biological process, including DNA binding, chromatin, growth, and development. The result of the KEGG pathway enrichment analysis showed that there are 7 KEGG pathways that were significantly co?enriched in forest musk deer and other species.These include protein families: genetic information processing, transcription factors, chromosome and associated proteins, spliceosome, transcription machinery, Notch signaling pathway, and maturity?onset diabetes of the young. By analyzing the SSR-containing key immune genes and their associated KEGG pathways in the CDS region of forset musk deer, 10 SSR-containing key immune genes corresponding to the KEGG pathway were found to be closely associated with the disease.
Key words： Forest musk deer; Siberian musk deer; Red deer; Small suede; Red muntjac; CDS; SSR; Functional analysis
Qi ZHAO , Qi ZHANG , Haoling LI , Yue LAN , Xingan YAN , Guijun ZHAO , Wenhua QI . Distinct patterns of microsatellite and functional analysis of forest musk deer and its closely related species[J]. ACTA THERIOLOGICA SINICA, 2022 , 42(6) : 705 -715 . DOI: 10.16829/j.slxb.150645
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