Inner Mongolia Agricultural University / Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, 010018, China.
Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, China.
BMC Genomics. 2020 Jan 31;21(1):108. doi: 10.1186/s12864-020-6495-2.
Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuable musk and meat, habitat losses, and forest fire. At present, this species is categorized as Vulnerable on the IUCN Red List. However, the genetic information of Siberian musk deer is largely unexplored.
Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp. We annotated 19,363 protein-coding genes and estimated 44.44% of the genome to be repetitive. Our phylogenetic analysis reveals that wild Siberian musk deer is closer to Bovidae than to Cervidae. Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments. We sequenced two additional genomes of Siberian musk deer constructed demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Finally, we identified several candidate genes that may play a role in the musk secretion based on transcriptome analysis.
Here, we present a high-quality draft genome of wild Siberian musk deer, which will provide a valuable genetic resource for further investigations of this economically important musk deer.
作为七珍之一的西伯利亚麝香鹿分布于亚洲的针叶林。由于非法猎捕获取有商业价值的麝香和鹿肉、栖息地丧失以及森林火灾，全球范围内西伯利亚麝香鹿的种群数量受到严重威胁。目前，该物种在 IUCN 红色名录中被列为易危。然而，关于西伯利亚麝香鹿的遗传信息尚未得到充分研究。
本研究组装了野生西伯利亚麝香鹿的基因组草图，大小为 31 亿碱基对，N50 为 29145bp， scaffolds 的 N50 为 7955248bp。注释得到了 19363 个蛋白质编码基因，估计基因组的 44.44%为重复序列。系统发育分析表明，野生西伯利亚麝香鹿与牛科的亲缘关系更近，而不是与鹿科。比较分析表明，西伯利亚麝香鹿的遗传特征适应了寒冷和高海拔环境。我们还对另外两个西伯利亚麝香鹿基因组进行了测序，构建了种群历史动态，表明有效种群大小的变化与最近的冰期相对应。最后，我们基于转录组分析鉴定了几个可能在麝香分泌中起作用的候选基因。
本研究提供了野生西伯利亚麝香鹿的高质量基因组草图，这将为进一步研究这种具有重要经济价值的麝香鹿提供有价值的遗传资源。
