Abstract:

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

摘要：

麝科和鹿科动物均属于偶蹄反刍类动物，具有重要的经济价值。通过系统的微卫星序列 (Simple sequences repeats, SSRs) 从基因组水平揭示物种间的系统进化关系，探索微卫星序列的基因功能及其富集的信号通路，目前仍缺乏相关研究。随着林麝 (Moschus berezovskii)、原麝 (Moschus moschiferus)、小麂 (Muntiacus reevesi)、赤麂 (Muntiacus vaginalis) 和马鹿 (Cervus elaphus) 基因组测序的完成，本文利用生物信息学方法提取了这些动物蛋白质编码区 (coding sequences, CDS) 序列，统计和分析了其CDS区微卫星序列分布规律及其生物学功能，探索了含SSR 基因富集的信号通路及其与疾病的关联性。结果表明，林麝、原麝、小麂、赤麂和马鹿蛋白质编码区含SSR序列的基因所占比例分别为6.96% (1 696个)、7.18% (2 359个)、7.29% (3 005个)、7.36% (1 916个) 和7.48% (1 924个)，并且这5种动物CDS区SSRs分布模式具有相似性，均是三倍体核苷酸 (即三核苷酸和六核苷酸) SSRs最多，分别为96.85%、94.87%、65.44%、64.23%和88.04%。GO功能富集表明，林麝与其他4种动物蛋白质编码区SSR序列在分子功能、细胞组成和生物学过程3个方面具有较多共同显著富集的功能，包括DNA结合、染色质和生长发育等。KEGG 通路分析表明，林麝及其他4种动物蛋白质编码区SSR序列具有7个共同显著富集的KEGG通路，包括遗传信息调控蛋白家族、转录因子、染色体及相关蛋白、剪接体、转录机制和Notch信号通路和成体糖尿病。通过对林麝编码区含SSR关键免疫基因及其相关联的KEGG通路进行分析，发现10个含SSR的关键免疫基因对应的KEGG通路与疾病密切相关。

关键词: 林麝, 原麝, 小麂, 赤麂, 马鹿, 编码区, 微卫星序列, 功能注释