Abstract
BackgroundSiberian 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.ResultsHere, 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.ConclusionsHere, 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.
Highlights
Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia
Evaluation Genomic DNA extracted from a female wild Siberian musk deer (WSMD) was subjected to shotgun sequencing using the Illumina Hiseq Xten platform
A total of 326.64 Gb (102.97× coverage) raw data were generated from all constructed libraries, from which 283.22Gb of clean data was obtained after removal of low-quality reads, duplicates, adaptors, and reads with more than 10% N bases
Summary
One of the seven species, is distributed in coniferous forests of Asia. 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. Recent work has provided the first complete genome sequence of the forest musk deer [49]. The population size of Siberian musk deer is dwindling rapidly by the same reasons as other musk species, and they have been categorized as Vulnerable on the IUCN Red List [51]. The whole-genome sequencing of Siberian musk deer has not been performed, and their potential value has yet to be discovered
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