The genome of the Chinese crocodile lizard; Shinisaurus crocodilurus
Dataset type: Genomic
Data released on June 02, 2017
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.
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):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|shinisaurus_crocodilurus||52224||Chinese crocodile lizard||Shinisaurus crocodilurus|| Description:The genomic DNA of the Chinese crocodi...|
Geographic location (latitude and longitude):not r...
... Description:The genomic DNA of the Chinese crocodile lizard was extracted from the blood collected from the tail vein of a single adult male lizard in Ocean Park Hong Kong which is a zoological theme park in Hong Kong.
Geographic location (latitude and longitude):not recorded
Geographic location (country and/or sea,region):Ocean Park Hong Kong
Collection date:Sat Oct 01 00:00:00 HKT 2011
Sample collection device or method:The venipuncture procedure was identical to that used for routine clinical blood draws in lizards in compliance with Animal Welfare and Use guidelines of Ocean Park.
Amount or size of sample collected:3.0 milliliter
Funding source:the China National Genebank
Alternative names:Chinese crocodile lizard
Sample source:Ocean Park Hong Kong
Sample contact:Dr.Paolo Martelli,Veterinary Department, Ocean Park Hong Kong, Hong Kong SAR.
Collected by:Dr.Paolo Martelli