The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.
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DOI：
10.1093/gbe/evy058
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发表时间：
2018-04-01
影响因子：
3.3
通讯作者：
Rüber L
中科院分区：
文献类型：
--
作者：
Malmstrøm M;Britz R;Matschiner M;Tørresen OK;Hadiaty RK;Yaakob N;Tan HH;Jakobsen KS;Salzburger W;Rüber L
世界上最小的鱼属于鲤属。这些小型鱼类是一个极端栖息地的特有物种：东南亚的泥炭沼泽森林，以高酸性黑水为特征。这一受威胁的栖息地是大量鱼类的家园，包括一些小型化但发育不全的物种。特别是亚棘鲤属的特征是深度的、全生物体的发育截短，导致性成熟的个体长度<8 mm，具有幼虫表型。在这里，我们报告的进化简化的基因组中的两个物种的侏儒小鱼属adrocypris使用全基因组测序。这两个物种的特点是前所未有的Hox基因丢失和基因组减少与他们的大规模发展截断。我们还展示了其他参与肌肉组织，神经系统和骨骼发育的基因在Aridocypris中是如何丢失的，反映了其高度的遗传表型。此外，我们的分析表明，两种机制，负责基因组流线型在Aridocypris与其他Cypriniformes：严重的内含子缩短和减少重复内容。作为第一份关于脊椎动物物种基因组序列的报告，我们的工作结果增强了我们对基因组进化以及基因型如何转化为表型的理解。此外，作为一个与斑马鱼密切相关的自然简化系统，Aridocypris为脊椎动物的发育提供了新的见解。
The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.
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影响因子：
7
作者：
Amores, A;Suzuki, T;Postlethwait, JH
通讯作者：
Postlethwait, JH
转座元件对四种硬骨鱼基因组大小变化的贡献
影响因子：
4.9
作者：
Gao B;Shen D;Xue S;Chen C;Cui H;Song C
通讯作者：
Song C
影响因子：
6.5
作者：
Chakrabarty, Prosanta;Faircloth, Brant C.;Alfaro, Michael E.
通讯作者：
Alfaro, Michael E.
影响因子：
14.9
作者：
Cunningham F;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Johnson N;Juettemann T;Kähäri AK;Keenan S;Martin FJ;Maurel T;McLaren W;Murphy DN;Nag R;Overduin B;Parker A;Patricio M;Perry E;Pignatelli M;Riat HS;Sheppard D;Taylor K;Thormann A;Vullo A;Wilder SP;Zadissa A;Aken BL;Birney E;Harrow J;Kinsella R;Muffato M;Ruffier M;Searle SM;Spudich G;Trevanion SJ;Yates A;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
3.3
作者：
Chalopin D;Naville M;Plard F;Galiana D;Volff JN
通讯作者：
Volff JN