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Data released on March 26, 2018

Supporting data for "The draft genome sequence of forest musk deer (Moschus berezovskii)"

Fan, Z; Li, W; Jin, J; Cui, K; Yan, C; Peng, C; Jian, Z; Bu, P; Price, M; Zhang, X; Shen, Y; Li, J; Qi, W; Yue, B (2018): Supporting data for "The draft genome sequence of forest musk deer (Moschus berezovskii)" GigaScience Database. http://dx.doi.org/10.5524/100411 RIS BibTeX Text

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.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA317652

Accessions (data not in GigaDB):

BioProject: PRJNA289641
BioProject: PRJNA289642

Keywords:

annotation phylogeny forest musk deer whole genome sequencing genome assembly 

Genomic

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Funding:

  • Funding body - Ministry of Science and Technology
  • Award ID - 2016YFC0503200
  • Comment - National Key Program of Research and Development
  • Awardee - B Yue

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN0462266668408 Chinese forest musk deerMoschus berezovskii Alternative names:musk deer
Description:Genomic DNA extracted from male Moschu...
Alternative accession-BioProject:PRJNA317652
...
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Phylogenetic treeUNKNOWN0.41 KB2018-02-01
otherTAR14.42 MB2018-02-01
Repeat sequenceGFF167.3 MB2018-02-01
otherTSV18.7 KB2018-02-01
otherTSV18.53 KB2018-02-01
AlignmentsBAM6.71 GB2018-02-01
Coding SequenceFASTA35.39 MB2018-02-01
Sequence assemblyFASTA701.11 MB2018-02-01
annotationGFF46.13 MB2018-02-01
protein sequenceFASTA13.19 MB2018-02-01
Displaying 1-10 of 14 File(s).

History:

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