The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus

Dataset type: Genomic
Data released on June 02, 2017

Gao J; Li Q; Wang Z; Zhou Y; Martelli P; Li F; Xiong Z; Wang J; Yang H; Zhang G (2017): The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus GigaScience Database.


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.

Additional details

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Accessions (data referenced by this study):

BioProject: PRJNA353147

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).

Date Action
June 3, 2017 Dataset publish
September 11, 2017 File Shinisaurus_crocodilurus.fa.gz updated
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix041