Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus.
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus.
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测序，从头组装和注释濒临灭绝的中国鳄鱼蜥蜴shinisaurus鳄鱼的基因组。
DOI：
10.1093/gigascience/gix041
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发表时间：
2017-07-01
期刊：
影响因子：
9.2
通讯作者：
Zhang G
中科院分区：
文献类型：
--
作者：
Gao J;Li Q;Wang Z;Zhou Y;Martelli P;Li F;Xiong Z;Wang J;Yang H;Zhang G
中国鳄蜥是鳞目下单种科的唯一现存代表。它是一种专性的半水生，胎生，昼夜活动的物种，仅限于中国西南部和越南东北部的山区的特定部分。然而，在过去的几十年里，由于非法偷猎和栖息地破坏，该物种的种群数量迅速减少，使这种独特的爬行动物物种濒临灭绝，并自1990年以来被列入《濒危野生动植物种国际贸易公约》附录II。2016年缔约方大会第十七届会议通过了《濒危野生动植物种国际贸易公约》将其列入附录一的提案。为了促进这一物种的保护，我们在Illumina HiSeq 2000平台上使用全基因组猎枪策略对一只雄性中华鳄蜥的基因组进行了测序。总共，我们从13个文库中产生了291 GB的原始测序数据(×149深度)，插入片段大小从250bp到40kb不等。经过聚合酶链式反应重复和低质量读取的筛选，获得了用于基因组组装的137G的∼干净数据(×70深度)。我们得到了一个总长度为2.24 GB的草稿基因组组装，N50支架大小为1.47Mb。重组基因组预测包含20,150个蛋白质编码基因和高达1114 Mb(49.6%)的重复元件。中国鳄蜥的基因组资源将有助于破译这种生物的生物学，并为保护工作提供必要的工具。这也为进一步研究鳞片类的演化提供了宝贵的资源。
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.
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DOI：
10.1126/science.1254449
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Green RE;Braun EL;Armstrong J;Earl D;Nguyen N;Hickey G;Vandewege MW;St John JA;Capella-Gutiérrez S;Castoe TA;Kern C;Fujita MK;Opazo JC;Jurka J;Kojima KK;Caballero J;Hubley RM;Smit AF;Platt RN;Lavoie CA;Ramakodi MP;Finger JW Jr;Suh A;Isberg SR;Miles L;Chong AY;Jaratlerdsiri W;Gongora J;Moran C;Iriarte A;McCormack J;Burgess SC;Edwards SV;Lyons E;Williams C;Breen M;Howard JT;Gresham CR;Peterson DG;Schmitz J;Pollock DD;Haussler D;Triplett EW;Zhang G;Irie N;Jarvis ED;Brochu CA;Schmidt CJ;McCarthy FM;Faircloth BC;Hoffmann FG;Glenn TC;Gabaldón T;Paten B;Ray DA
通讯作者：
Ray DA
影响因子：
7
作者：
She, Rong;Chu, Jeffrey S. -C.;Chen, Nansheng
通讯作者：
Chen, Nansheng
中国鳄蜥（Shinisaurus crocodilurus）的遗传多样性和种群统计
影响因子：
3.7
作者：
Huang H;Wang H;Li L;Wu Z;Chen J
通讯作者：
Chen J
影响因子：
64.8
作者：
Fry, BG;Vidal, N;Kochva, E
通讯作者：
Kochva, E
影响因子：
14.9
作者：
Bairoch, A;Apweiler, R
通讯作者：
Apweiler, R