The draft genome sequence of forest musk deer (Moschus berezovskii)

Abstract

BackgroundThe forest musk deer, Moschus berezovskii, is one of seven musk deer (Moschus spp.) and is distributed in Southwest China. Akin to other musk deer, the forest musk deer has been traditionally and is currently hunted for its musk (i.e., global perfume industry). Considerable hunting pressure and habitat loss have caused significant population declines. Consequently, the Chinese government commenced captive breeding programs for musk harvesting in the 1950s. However, the prevalence of fatal diseases is considerably restricting population increases. Disease severity and extent are exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential that knowledge of captive and wild forest musk deer populations' immune system and genome be gained in order to improve their physical and genetic health. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses.FindingsA total of 407 Gb raw reads from whole-genome sequencing were generated using the Illumina HiSeq 4000 platform. The final genome assembly is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length of 2.85 Mb. We identified 24,352 genes and found that 42.05% of the genome is composed of repetitive elements. We also detected 1,236 olfactory receptor genes. The genome-wide phylogenetic tree indicated that the forest musk deer was within the order Artiodactyla, and it appeared as the sister clade of four members of Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage.ConclusionsWe provide the first genome sequence and gene annotation for the forest musk deer. The availability of these resources will be very useful for the conservation and captive breeding of this endangered and economically important species and for reconstructing the evolutionary history of the order Artiodactyla.

The olfactory subgenome and specific odor recognition in forest musk deer

“…The whole genome sequence of the forest musk deer was sequenced and assembled by our laboratory (Fan et al . ). The G protein‐coupled receptorsuperfamily non‐OR protein sequence (NP_000667) that was used as an outgroup to construct phylogenetic trees was downloaded from GenBank.…”

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

“…We compared the genome assembly of the Siberian musk deer and forest musk deer recently reported by Fan et al [55] (Additional file 3: Table S17). The continuity of our assembly was remarkably increased compared with that of the forest musk deer genome assembly, particularly in regard to the scaffold N50 (7.95 vs 2.85 Mb) and scaffold number (13,344 vs 79,206).…”

Organization of the Addax Major Histocompatibility Complex Provides Insights Into Ruminant Evolution

“…The accession numbers of the genes used in the construction of the phylogenetic tree are shown in Table S2. Sequences of the MHC class II genes of the forest musk deer (Moschus berezovskii) were acquired by a local BLAST search of the sequencing data reported by Fan et al (44). The divergence time of the MHC genes was estimated using BEAST (45), with a relaxed molecular clock.…”