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.
Highlights
The Chinese crocodile lizard, Shinisaurus crocodilurus (NCBI taxonomy ID 52224) (Fig. 1), was first collected in 1928
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
The assembled genome was predicted to contain 20 150 protein-coding genes and up to 1114 Mb (49.6%) of repetitive elements
Summary
The Chinese crocodile lizard, Shinisaurus crocodilurus (NCBI taxonomy ID 52224) (Fig. 1), was first collected in 1928. The species usually is found along slow-flowing rocky streams in montane evergreen forests [2] and is distributed in the east part of the Guangxi Zhuang Autonomous Region, the west and north parts of Guangdong Province in southern China, and in mountainous areas of northern Vietnam [3] It is a semiaquatic diurnal predator and a strong swimmer, preying on fish, tadpoles, and aquatic insects. The end result was a genome assembly with a total length of 2.24 Gb, scaffold and contig N50s of 1470 kb and 11.7 kb, respectively, and unclosed gap regions representing 7.98% of the assembly, which is comparable to the previously published reptile genome assemblies (Table 3). We ran the same version of BUSCO to the other 14 retile genomes, respectively; the completeness of the Chinese crocodile lizard assembly was comparable to other published reptile genome assemblies (Table 4)
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