Background: 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. Results: 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. Conclusions: 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.

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Background: Musk deer is famous for its secretion of musk, but due to various factors that the musk deer population has dropped sharply and it is difficult to expand herd sizes.In light of the rapid development of animal husbandry and scientific technology, as well as the urgent need for wildlife conservation, research on the gut microbiota of musk deer is warranted. The gut microbiota is a complex ecosystem that is regulated by many factors, such as dietary, environmental, host factors, and seasonal changes. Results: We studied the gut microbiota in Siberian and Forest musk deer using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene. Fecal samples were collected during two seasons to determine associations between community diversity, composition, and seasonal factors. The results showed that the Firmicutes and Bacteroidetes were the predominant phyla in Siberian and Forest musk deer , their relative abundance was significantly different with species and seasonal factors. The Siberian musk deer population sampled in this study had a wider feeding range and no dietary limitations. Affected by the type of food sources and the feed intake , the microbial α-diversity is higher in summer than winter. Conclusions: The gut bacterial composition of these two musk deer is significantly different, and the abundance between core bacteria is affected by seasonal factors. This study is the first to analyze the composition of the gut microflora in Siberian musk deer, and these results provide a foundation for improving feeding for musk deer populations and further studies investigating the environmental impact of musk deer.

Background: Musk deer is famous for its secretion of musk, but due to various factors that the musk deer population has dropped sharply and it is difficult to expand herd sizes. In light of the rapid development of agriculture and technology, as well as the urgent need for wildlife conservation, research on the gut microbiota of musk deer is warranted. The gut microbiota impacts host health is shaped by dietary, environmental, and host factors.Results: We studied the gut microbiota in Siberian musk and Forest musk deer using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene. Fecal samples were collected during two seasons to determine associations between community diversity, composition, and seasonal factors. The results show that the Firmicutes and Bacteroidetes were the predominant phyla in both species, their relative abundance was significantly different with species and seasonal factors. The Siberian musk deer population sampled in this study had a wider feeding range and no dietary limitations. Affected by the richness and type of food sources, the microbial α-diversity is higher in summer than winter. In the siberian musk deer have only Tenericutes significant difference with the season change. Conclusions:The gut bacterial composition of these two musk deer is significantly different, and the abundance of core bacteria is affected by seasonal factors. This study is the first to analyze the composition of the gut microflora in Siberian musk deer, and these results provide a foundation for improving feeding for musk deer populations and further studies investigating the environmental impact of musk deer.