Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.
Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.
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DOI：
10.1093/molbev/msad188
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发表时间：
2023-09-01
影响因子：
10.7
通讯作者：
Kingsley, David M.
中科院分区：
文献类型：
--
作者：
Chen, Heidi I.;Turakhia, Yatish;Bejerano, Gill;Kingsley, David M.
关键词：
鳍是鱼类的主要功能性附属物，在不同的谱系中被反复修改。为了寻找自然鳍多样性背后的基因组变化，我们比较了36种percomorph鱼类的基因组，这些鱼类跨越了1亿多年的进化，具有完整或减少的骨盆和尾鳍。我们确定了1,614个基因组区域，这些区域在鳍完整物种中非常保守，但在多个鳍减少的谱系中缺失。在野生鳍减少物种的保守序列的经常性缺失丰富的附属物的发展相关的功能，表明收敛鳍减少在生物体水平与鳍附属物发展基因附近的重复基因组缺失。我们使用测序和功能增强子测定来证实PelA，以前与棘鱼的复发性骨盆损失相关的Pitx 1增强子，也被独立删除，可能有助于远亲骨盆减少物种的鳍形态。我们还确定了一种新的增强子，它在大多数percomorphs中是保守的，在转基因棘鱼中驱动尾鳍表达，在具有尾鳍减少的tetraodontiform，syngnathid和synbranchid物种中缺失，并且当通过基因组编辑靶向时改变尾鳍发育。我们的研究说明了一种广泛适用的策略，用于将表型映射到脊椎动物物种树的基因型，并突出了在1亿年的鱼类进化中用于进化经常性表型的调控基因组热点的显着新例子。
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
影响因子：
16.8
作者：
Alfaro, Michael E.;Faircloth, Brant C.;Near, Thomas J.
通讯作者：
Near, Thomas J.
影响因子：
56.9
作者：
FRENCH, V;BRYANT, PJ;BRYANT, SV
通讯作者：
BRYANT, SV
影响因子：
10.7
作者：
Chikina, Maria;Robinson, Joseph D.;Clark, Nathan L.
通讯作者：
Clark, Nathan L.