Help Login Create account

Data released on December 20, 2017

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

Zhang, C; Chen, L; Zhou, Y; Wang, K; Chemnick, L, G; Ryder, O, A; Wang, W; Zhang, G; Qiu, Q (2017): Supporting data for "Draft genome of the milu (Elaphurus davidianus)" GigaScience Database. http://dx.doi.org/10.5524/100383 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix130

Accessions (data included in GigaDB):

BioProject: PRJNA391565

Projects:


Genomic

http://gigadb.org/images/data/cropped/100383.jpg

Funding:

  • Funding body - Northwestern Polytechnical University
  • Comment - Talents Team Construction Fund
  • Funding body - Northwestern Polytechnical University
  • Comment - Talents Team Construction Fund

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDFile TypeFile FormatSizeRelease Date 
otherUNKNOWN0.1 KB2017-11-13
annotationGFF203.05 KB2017-11-13
ReadmeTEXT2.64 KB2017-11-13
annotationGFF226.31 MB2017-11-13
annotationGFF35.72 KB2017-11-13
mixed archiveTAR6.41 KB2017-11-13
annotationGFF245.64 KB2017-11-13
annotationGFF82.85 KB2017-11-13
Displaying 11-18 of 18 File(s).

History:

+

Other datasets you might like: