Genomic data of the Chinese tree shrew (Tupaia chinensis).

Dataset type: Genomic
Data released on April 11, 2014

Fan Y; Huang Z; Cao C; Chen C; Chen Y; Fan D; He J; Hou H; Hu L; Hu X; Jiang X; Lai R; Lang Y; Liang B; Liao S; Mu D; Ma Y; Niu Y; Sun X; Xia J; Xiao J; Xiong Z; Xu L; Yang L; Zhang Y; Zhao W; Zhao X; Zheng Y; Zhou J; Zhu Y; Zhang G (2014): Genomic data of the Chinese tree shrew (Tupaia chinensis). GigaScience Database.


Chinese tree shrews (Tupaia belangeri chinensis) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly support its close affinity to primates.

DNA form the tree shrew was collected in Yunnan, China. We sequenced the 3.2 Gb genome to a depth of approximately 79.2x with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb).
The assembled scaffolds of high quality sequences total 253.5 Gb, with the contig and scaffold N50 values of 22 kb and 3.65 Mb respectively. We identified 22,063 protein-coding genes.
Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).

Additional details

Read the peer-reviewed publication(s):

(PubMed: 23385571)

Accessions (data generated as part of this study):

BioProject: PRJNA169406


Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS347509246437Tupaia chinensisChinese tree shrewTupaia chinensis Sex:male [PATO:0000384]
Geographic location (country and/or sea,region):Ch...
Geographic location (latitude and longitude):not r...
Displaying 1-1 of 1 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT0.38 KB2014-04-11
SRS347509AnnotationGFF40.91 MB2014-04-11
SRS347509Coding sequenceFASTA26.41 MB2014-04-11
SRS347509Sequence assemblyFASTA2.67 GB2014-04-11
SRS347509Protein sequenceFASTA9.81 MB2014-04-11
Displaying 1-5 of 5 File(s).
Date Action