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Data released on June 02, 2017

The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus

Gao, J; Li, F; Li, Q; Martelli, P; Wang, J; Wang, Z; Xiong, Z; Yang, H; Zhang, G; Zhou, Y (2017): The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus GigaScience Database. http://dx.doi.org/10.5524/100315 RIS BibTeX Text

The Chinese crocodile lizard, Shinisaurus crocodilurus, is the only living representative of the monotypic family Shinisauridae under the order Squamata. It is an obligate semi-aquatic, viviparous, diurnal species restricted to specific portions of mountainous locations in southwestern China and northeastern Vietnam. However, in the past several decades, this species has undergone a rapid decrease in population size due to illegal poaching and habitat disruption, making this unique reptile species endangered and listed in CITES Appendix II since 1990. A proposal to uplist it to Appendix I was passed at the CITES CoP17 in 2016.
To promote the conservation of this species, we sequenced the genome of a male Chinese crocodile lizard using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform. In total, we generated ~291Gb raw sequencing data (149X depth) from 13 libraries with insert sizes ranging from 250 bp to 40 kb. After filtering for PCR-duplicated and low-quality reads, ~137 Gb clean data (70X depth) were obtained for genome assembly. We yielded a draft genome assembly with a total length of 2.24 Gb and an N50 scaffold size of 1.47 Mb. The assembled genome was predicted to contain 20,150 protein-coding genes and up to 1,114 Mb (49.6%) of repetitive elements.
The genomic resource of the Chinese crocodile lizard will contribute to deciphering the biology of this organism and provides an essential tool for conservation efforts. It also provides a valuable resource for future study of squamate evolution.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix041

Accessions (data not in GigaDB):

BioProject: PRJNA353147

Keywords:

Chinese crocodile lizard, Shinisaurus crocodilurus, sequencing, genome assembly, annotation 

Genomic

http://gigadb.org/images/data/cropped/100315.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
shinisaurus_crocodilurus52224Chinese crocodile lizard Shinisaurus crocodilurus Description:The genomic DNA of the Chinese crocodi...
Alternative accession-BioSample:SAMN06014616
Geographic location (latitude and longitude):not r...
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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 
Coding sequenceFASTA9.57 MB2017-05-29
annotationFASTA71.1 MB2017-05-29
protein sequenceFASTA6.14 MB2017-05-29
Genome sequenceFASTA615.63 MB2017-05-29
annotationGFF15.98 MB2017-05-29
annotationGFF16.31 MB2017-05-29
annotationGFF359.91 KB2017-05-29
annotationGFF252.22 MB2017-05-29
annotationGFF2.13 MB2017-05-29
annotationGFF46.44 MB2017-05-29
Displaying 1-10 of 52 File(s).

History:

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