Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles.
Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles.
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DOI：
10.1534/g3.120.401440
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发表时间：
2020-12-03
期刊：
影响因子：
--
通讯作者：
Rhen T
中科院分区：
文献类型：
--
作者：
Das D;Singh SK;Bierstedt J;Erickson A;Galli GLJ;Crossley DA 2nd;Rhen T
海龟是标志性的爬行动物，生活在从海洋到沙漠的一系列生态系统中，从热带到北部温带地区的气候。然而，我们对海龟在如此多样化的环境中生存和繁殖的遗传适应知之甚少。常见的蛇龟是研究气候适应的理想模式物种，因为它们广泛分布于北美的热带到北温带。它们也很容易在圈养条件下维护和繁殖，并产生较大的窝点，这使得它们适合对温度相关的性别决定等特征进行量化遗传和分子遗传学研究。因此，我们建立了一个圈养繁殖群体，并使用短读和长读对一只雌性大熊猫的DNA进行了测序。在修剪和过滤之后，我们有209.51 GB的Illumina读取、25.72 GB的PacBio读取和21.72 GB的Nanopore读取。组装的基因组大小为2.258 GB，有13,224个支架，N50为5.59Mb。最长的支架为27.24Mb。Busco分析显示，97.4%的核心脊椎动物基因在基因组中。我们在参照龟中发现了327万个SNPs，这表明个体杂合性水平相对较高。我们使用RNA-Seq数据组装了转录组，并使用基因预测软件产生了22,812个蛋白质编码基因模型。甲鱼基因组的质量和邻接性与大多数已发表的爬行动物基因组相似或更好。这里确定的基因组和遗传变异为未来的气候适应研究提供了基础。
Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of traits like temperature-dependent sex determination. We therefore established a captive breeding colony and sequenced DNA from one female using both short and long reads. After trimming and filtering, we had 209.51Gb of Illumina reads, 25.72Gb of PacBio reads, and 21.72 Gb of Nanopore reads. The assembled genome was 2.258 Gb in size and had 13,224 scaffolds with an N50 of 5.59Mb. The longest scaffold was 27.24Mb. BUSCO analysis revealed 97.4% of core vertebrate genes in the genome. We identified 3.27 million SNPs in the reference turtle, which indicates a relatively high level of individual heterozygosity. We assembled the transcriptome using RNA-Seq data and used gene prediction software to produce 22,812 models of protein coding genes. The quality and contiguity of the snapping turtle genome is similar to or better than most published reptile genomes. The genome and genetic variants identified here provide a foundation for future studies of adaptation to climate.
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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：
9.8
作者：
Cao, Dainan;Wang, Meng;Gong, Shiping
通讯作者：
Gong, Shiping
影响因子：
14.9
作者：
Chakraborty, Mahul;Baldwin-Brown, James G.;Emerson, J. J.
通讯作者：
Emerson, J. J.
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
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。
影响因子：
9.2
作者：
Gao J;Li Q;Wang Z;Zhou Y;Martelli P;Li F;Xiong Z;Wang J;Yang H;Zhang G
通讯作者：
Zhang G