Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus

CORC > 昆明动物研究所 > 昆明动物研究所 > 遗传资源与进化国家重点实验室

	Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus
	Gao J 1,2,3; Li QY 2,3,4; Li F 2,3; Xoing ZJ 2,3,4; Wang J 3,7; Yang HM 3,7; Zhang GJ *2,3,4,8; Wang ZJ 2,3,5; Zhou Y 2,3; Martelli P 6
刊名	Gigascience
	2017
卷号	期号:页码:Epub ahead of print
关键词	Chinese Crocodile Lizard Shinisaurus Crocodilurus Annotation Genome Assembly Sequencing
英文摘要	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 1114 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.
语种	英语
资助机构	This work was funded by the China National Genebank, and the Project U1301252 supported by National Natural Science Foundation of China. ; This work was funded by the China National Genebank, and the Project U1301252 supported by National Natural Science Foundation of China.
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/11740]
专题	昆明动物研究所_遗传资源与进化国家重点实验室昆明动物研究所_基因起源组
作者单位	1.BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China 2.China National Genebank, BGI-Shenzhen, Shenzhen 518083, China 3.BGI-Shenzhen, Shenzhen 518083, China 4.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 5.Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria 6.Veterinary Department, Ocean Park Hong Kong, Hong Kong SAR 7.James D. Watson Institute of Genome Sciences, Hangzhou 310058, China 8.Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
推荐引用方式 GB/T 7714	Gao J,Li QY,Li F,et al. Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus[J]. Gigascience,2017,():Epub ahead of print.
APA	Gao J.,Li QY.,Li F.,Xoing ZJ.,Wang J.,...&Martelli P.(2017).Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus.Gigascience,(),Epub ahead of print.
MLA	Gao J,et al."Sequencing, de novo assembling and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus".Gigascience .(2017):Epub ahead of print.