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Gigascience. 2017 Jul 1;6(7):1-6. doi: 10.1093/gigascience/gix041.

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

Gao J1,2,3, Li Q2,3,4, Wang Z2,3,5, Zhou Y2,3, Martelli P6, Li F2,3, Xiong Z2,3,4, Wang J3,7, Yang H3,7, Zhang G2,3,4,8.

Author information

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.

Abstract

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 the Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendix II since 1990. A proposal to uplist it to Appendix I was passed at the Convention on International Trade in Endangered Species of Wild Fauna and Flora Seventeenth meeting of the Conference of the Parties 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 ∼291 Gb of raw sequencing data (×149 depth) from 13 libraries with insert sizes ranging from 250 bp to 40 kb. After filtering for polymerase chain reaction-duplicated and low-quality reads, ∼137 Gb of clean data (×70 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.

KEYWORDS:

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

PMID:
28595343
PMCID:
PMC5569961
DOI:
10.1093/gigascience/gix041
[Indexed for MEDLINE]
Free PMC Article

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