The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus

Dataset type: Genomic
Data released on June 02, 2017

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

DOI10.5524/100315

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

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





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).




File NameSample IDData TypeFile FormatSizeRelease Date 
annotationFASTA71.1 MB2017-05-29
annotationIPR268.3 KB2017-05-29
annotationGFF2.13 MB2017-05-29
annotationIPR4.52 MB2017-05-29
annotationGFF161.92 MB2017-05-29
annotationUNKNOWN201.44 MB2017-05-29
annotationIPR232.77 KB2017-05-29
annotationWEGO107.71 KB2017-05-29
annotationIPR407.52 KB2017-05-29
annotationUNKNOWN14.73 MB2017-05-29
Displaying 1-10 of 52 File(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