Genomic data of the Chinese alligator (Alligator sinensis).

Dataset type: Genomic
Data released on March 28, 2014

Wan Q; Pan S; Hu L; Zhu Y; Xu P; Xia J; Chen H; He G; He J; Ni X; Hou H; Liao S; Yang H; Chen Y; Gao S; Ge Y; Cao C; Li P; Fang L; Liao L; Zhang S; Wang M; Dong W; Fang S (2014): Genomic data of the Chinese alligator (Alligator sinensis). GigaScience Database. http://dx.doi.org/10.5524/100077

DOI10.5524/100077

The Chinese alligator (Alligator sinensis), a freshwater crocodilian endemic to China, is one of the most endangered crocodilian species. Currently, there are ~100 Chinese alligators in the wild and ~10 000 captive individuals in Zhejiang and Anhui Provinces. We chose the Chinese alligator for genome sequencing with the hope of providing information that could help design scientific captive-breeding programs for population recovery project of this endangered species.
DNA from the chinese aligator was collected in Zhejiang Province, China. We sequenced the 2.3Gb genome with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 314Gb, with the contig and scaffold N50 values of 23.4kb and 2.2Mb respectively. We identified 22,200 protein-coding genes with an mean length of 1403bp.

Additional details

Read the peer-reviewed publication(s):

Wan, Q.-H., Pan, S.-K., Hu, L., Zhu, Y., Xu, P.-W., Xia, J.-Q., … Fang, S.-G. (2013). Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Research, 23(9), 1091–1105. doi:10.1038/cr.2013.104 (PubMed: 24165891)

Accessions (data generated as part of this study):

BioProject: PRJNA215016

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS47074238654Alligator sinensischinese alligatorAlligator sinensis Geographic location (country and/or sea,region):Ch...
Geographic location (latitude and longitude):not r...
IUCN Red List:Critically endangered
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
SRS470742AnnotationGFF18.74 MB2014-03-28
SRS470742Coding sequenceFASTA32.52 MB2014-03-28
SRS470742Sequence assemblyFASTA2.12 GB2014-03-28
SRS470742Protein sequenceFASTA12.05 MB2014-03-28
ReadmeUNKNOWN0.5 KB2014-03-28
Displaying 1-5 of 5 File(s).
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