The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
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DOI：
10.1038/ng.3526
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发表时间：
2016-04
期刊：
影响因子：
30.8
通讯作者：
Postlethwait JH
中科院分区：
文献类型：
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作者：
Braasch I;Gehrke AR;Smith JJ;Kawasaki K;Manousaki T;Pasquier J;Amores A;Desvignes T;Batzel P;Catchen J;Berlin AM;Campbell MS;Barrell D;Martin KJ;Mulley JF;Ravi V;Lee AP;Nakamura T;Chalopin D;Fan S;Wcisel D;Cañestro C;Sydes J;Beaudry FE;Sun Y;Hertel J;Beam MJ;Fasold M;Ishiyama M;Johnson J;Kehr S;Lara M;Letaw JH;Litman GW;Litman RT;Mikami M;Ota T;Saha NR;Williams L;Stadler PF;Wang H;Taylor JS;Fontenot Q;Ferrara A;Searle SM;Aken B;Yandell M;Schneider I;Yoder JA;Volff JN;Meyer A;Amemiya CT;Venkatesh B;Holland PW;Guiguen Y;Bobe J;Shubin NH;Di Palma F;Alföldi J;Lindblad-Toh K;Postlethwait JH
为了将人类生物学与鱼类生物医学模型联系起来，我们对斑点加(Lesssteus Oculatus)的基因组进行了测序，在硬骨基因组复制(TGD)之前，斑点加的血统从硬骨分化而来。缓慢进化的GAR基因组在内容和大小上保守，许多完整的染色体来自骨质脊椎动物的祖先。GAR通过阐明免疫、矿化和发育的进化(例如，Hox、ParaHox和miRNA基因)将硬骨鱼与四足动物联系起来。许多保守的非编码元件(CNE，通常是顺式调控的)在人与硬骨的直接比较中无法检测到，使用GAR变得明显：功能研究发现了这种神秘的CNES的保守角色，有助于注释在人类基因组范围的关联研究中识别的序列。转录分析表明，复制的硬骨基因的表达结构域和表达水平的总和往往与GAR基因的模式和水平相似，与亚功能化一致。GAR基因组为理解基因组复制后的进化、脊椎动物基因组的起源以及人类调控序列的功能提供了资源。
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before the teleost genome duplication (TGD). The slowly evolving gar genome conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and miRNA genes). Numerous conserved non-coding elements (CNEs, often cis-regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles of such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses revealed that the sum of expression domains and levels from duplicated teleost genes often approximate patterns and levels of gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes, and the function of human regulatory sequences.