Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity
Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity
复制标题
DOI：
10.1534/g3.119.400725
复制
发表时间：
2019-03
期刊：
影响因子：
--
通讯作者：
Y. Takehana;M. Zahm;Cédric Cabau;C. Klopp;Céline Roques;O. Bouchez;C. Donnadieu;Célia Barrachina;L. Journot;M. Kawaguchi;S. Yasumasu;Satoshi Ansai;K. Naruse;Koji Inoue;Chuya Shinzato;M. Schartl;Y. Guiguen;A. Herpin
中科院分区：
文献类型：
--
作者：
Y. Takehana;M. Zahm;Cédric Cabau;C. Klopp;Céline Roques;O. Bouchez;C. Donnadieu;Célia Barrachina;L. Journot;M. Kawaguchi;S. Yasumasu;Satoshi Ansai;K. Naruse;Koji Inoue;Chuya Shinzato;M. Schartl;Y. Guiguen;A. Herpin
Oryzias 属由 35 种青鳉鱼组成，每种都表现出各种生态、形态和生理特性和适应性。除了作为通过比较基因组方法研究性别决定、行为、形态或适应等多种性状的属内进化的综合系统发育群体之外，所有青鳉物种都具有实验模型生物的许多优点，包括体积小、世代时间短、透明的胚胎以及用于反向和正向遗传研究的基因组编辑工具。爪哇青鳉（Oryzias javanicus）是两种非常适合生活在咸水/海水中的青鳉之一。作为红树林生态系统的重要组成部分，爪哇 O. javanicus 也被用作生态毒理学研究的有价值的海洋试验鱼。在这里，我们对爪哇爪哇的整个基因组进行了测序和组装，并预计该资源将促进广泛的比较基因组、系统发育和功能研究。补充测序方法（包括长读长技术和与遗传图谱的数据集成）最终组装了 908 Mbp 的爪哇爪哇基因组。进一步分析估计爪哇爪哇基因组含有33%的重复序列，杂合度为0.96%。获得的组装草案包含 525 个支架，总长度为 809.7 Mbp，N50 为 6,3 Mbp，L50 为 37 个支架。我们鉴定了 21454 个预测转录本，总转录组大小分别为 57、146、583 bps。我们在这里提供了广盐爪哇鱼青鳉的高质量染色体规模基因组组装草案（锚定在24条染色体上的321个支架（占总碱基的97.7%）），并强调对盐度的进化适应。
The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.