Supporting data for "Draft genome of the milu (Elaphurus davidianus)"

Dataset type: Genomic
Data released on December 20, 2017

Zhang C; Chen L; Zhou Y; Wang K; Chemnick LG; Ryder OA; Wang W; Zhang G; Qiu Q (2017): Supporting data for "Draft genome of the milu (Elaphurus davidianus)" GigaScience Database.


Milu, also known as Père David’s deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena we constructed a draft genome of the species.
In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb), and total length of 2.52 Gb. Moreover, we identified 20,125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1,335 miRNA, 1,441 snRNA and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species- specific genes and 293 expanded gene families in the milu lineage.
We report the first reference genome of milu, which will provide a valuable resource for studying the species’ demographic history of severely bottlenecked and genetic mechanism of special phenotypic evolution.

Additional details

Read the peer-reviewed publication(s):

Zhang, C., Chen, L., Zhou, Y., Wang, K., Chemnick, L. G., Ryder, O. A., … Qiu, Q. (2017). Draft genome of the milu (Elaphurus davidianus). GigaScience, 7(2). doi:10.1093/gigascience/gix130

Accessions (data generated as part of this study):

BioProject: PRJNA391565


Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
milu-dafeng-00543332 Pere David's deerElaphurus davidianus Description:Genomic DNA was extracted from blood o...
Molecular data type:DNA
milu-zoo-00143332 Pere David's deerElaphurus davidianus Description:Genomic DNA was extracted from a male ...
Molecular data type:DNA
Displaying 1-2 of 2 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsFASTA8.76 MB2017-11-13
otherUNKNOWN0.1 KB2017-11-13
otherarchive184.27 MB2017-11-13
Coding SequenceFASTA9.65 MB2017-11-13
annotationGFF1.96 MB2017-11-13
protein sequenceFASTA6.31 MB2017-11-13
Genome sequenceFASTA2.39 GB2017-11-13
SNPsVCF404.81 MB2017-11-13
AlignmentsMAF1.33 GB2017-11-13
Phylogenetic treeUNKNOWN0.32 KB2017-11-13
Displaying 1-10 of 18 File(s).
Funding body Awardee Award ID Comments
Northwestern Polytechnical University Q Qiu Talents Team Construction Fund
Northwestern Polytechnical University W Wang Talents Team Construction Fund
Date Action
December 20, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix130