Supporting data for "The draft genome sequence of forest musk deer (Moschus berezovskii)"
Dataset type: Genomic
Data released on March 26, 2018
The 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 has caused significant population declines and therefore 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 is exacerbated by inbreeding and genetic diversity declines in captive musk deer populations. It is essential for the physical and genetic health of captive and wild forest musk deer populations to improve knowledge of its immune system and genome. We have thus sequenced the whole genome of the forest musk deer, completed the genomic assembly and annotation, and performed preliminary bioinformatic analyses. A total of 407 Gb raw reads from whole-genome sequencing was generated by the Illumina Hiseq4000 platform. The final assembly genome is around 2.72 Gb, with a contig N50 length of 22.6 kb and a scaffold N50 length 2.85 Mb. We identified 24,352 genes, and found 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 family Bovidae. In total, 576 genes were under positive selection in the forest musk deer lineage. We 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 for this Endangered and economically important species, and for reconstructing the evolutionary history of the order Artiodactyla.
Read the peer-reviewed publication(s):
Fan, Z., Li, W., Jin, J., Cui, K., Yan, C., Peng, C., … Yue, B. (2018). The draft genome sequence of forest musk deer (Moschus berezovskii). GigaScience, 7(4). doi:10.1093/gigascience/giy038
Accessions (data included in GigaDB):
Accessions (data not in GigaDB):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|SAMN04622666||68408||Chinese forest musk deer||Moschus berezovskii|| Alternative names:musk deer|
Description:Genomic DNA extracted from male Moschu...
... Alternative names:musk deer
Description:Genomic DNA extracted from male Moschus berezovskii sample from Miyaluo
Geographic location (country and/or sea,region):Miyaluo, Sichuan Province, China
Age:About 5 years old
Collected by:Mr. Guo Cai at Sichuan University
Environment (feature):forest farm
Environment (material):forest musk deer farm of the Miyaluo township, limited company of Pienztehuang of Sichuan Province, China
Estimated genome size:2.95Gb
Sample collection device or method:muscle tissue from a dead individual
Sample material processing:The tissue was stored at fridge (-80 ℃)
Amount or size of sample collected:About 5 kg
Specimen voucher:Sichuan University:M0761