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Data released on October 20, 2017

Draft genomic data of the Reindeer (Rangifer tarandus).

Li, Z; Lin, Z; Ba, H; Chen, L; Yang, Y; Wang, K; Qiu, Q; Wang, W; Li, G (2017): Draft genomic data of the Reindeer (Rangifer tarandus). GigaScience Database. http://dx.doi.org/10.5524/100370 RIS BibTeX Text

Reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovid milk. A high quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer.
We obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus.
Our results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix102

Keywords:

rangier tarandus whole genome sequencing assembly annotation 

Genomic

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Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 31501984
  • Awardee - Z Li
  • Funding body - Central Public-interest Scientific Institution Basal Research Fund
  • Award ID - 1610342016026
  • Awardee - Zhipeng Li
  • Funding body - Northwestern Polytechnical University
  • Comment - Talents Team Construction Fund
  • Awardee - Q Qiu; W Wang

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
reindeer_genomics_DNA9870cariboureindeerRangifer tarandus Description:Fresh blood was collectedfrom a two-ye...
Geographic location (latitude and longitude):50.77...
Geographic location (country and/or sea,region):Gr...
...
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Displaying 1-1 of 1 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 
Phylogenetic treeFASTA1.73 MB2017-10-17
otherTAR159.66 MB2017-10-17
annotationGFF53.62 MB2017-10-17
Coding SequenceFASTA31.93 MB2017-10-17
protein sequenceFASTA12.35 MB2017-10-17
annotationGFF5.78 MB2017-10-17
ReadmeTEXT2.57 KB2017-10-17
AlignmentsMAF1.42 GB2017-10-17
Genome sequenceFASTA761.69 MB2017-10-17
Phylogenetic treeUNKNOWN0.3 KB2017-10-17
Displaying 1-10 of 17 File(s).

History:

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