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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. 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.

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Read the peer-reviewed publication(s):

Gao, J., Li, Q., Wang, Z., Zhou, Y., Martelli, P., Li, F., … Zhang, G. (2017). Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. GigaScience, 6(7), 1–6. doi:10.1093/gigascience/gix041

Accessions (data not in GigaDB):

BioProject: PRJNA353147


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


Samples: Table Settings


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...
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings


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

File NameSample IDData TypeFile FormatSizeRelease Date 
annotationIPR268.3 KB2017-05-29
annotationGFF252.22 MB2017-05-29
annotationGFF161.92 MB2017-05-29
annotationUNKNOWN201.44 MB2017-05-29
annotationFASTA71.1 MB2017-05-29
annotationGFF359.91 KB2017-05-29
annotationUNKNOWN14.73 MB2017-05-29
annotationGFF16.31 MB2017-05-29
annotationGFF46.44 MB2017-05-29
annotationUNKNOWN57.38 MB2017-05-29
Displaying 41-50 of 52 File(s).



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