The genomic substrate for adaptive radiation in African cichlid fish.
The genomic substrate for adaptive radiation in African cichlid fish.
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DOI：
10.1038/nature13726
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发表时间：
2014-09-18
期刊：
影响因子：
64.8
通讯作者：
Di Palma, Federica
中科院分区：
文献类型：
--
作者：
Brawand, David;Wagner, Catherine E.;Li, Yang I.;Malinsky, Milan;Keller, Irene;Fan, Shaohua;Simakov, Oleg;Ng, Alvin Y.;Lim, Zhi Wei;Bezault, Etienne;Turner-Maier, Jason;Johnson, Jeremy;Alcazar, Rosa;Noh, Hyun Ji;Russell, Pamela;Aken, Bronwen;Alfoeldi, Jessica;Amemiya, Chris;Azzouzi, Naoual;Baroiller, Jean-Francois;Barloy-Hubler, Frederique;Berlin, Aaron;Bloomquist, Ryan;Carleton, Karen L.;Conte, Matthew A.;D'Cotta, Helena;Eshel, Orly;Gaffney, Leslie;Galibert, Francis;Gante, Hugo F.;Gnerre, Sante;Greuter, Lucie;Guyon, Richard;Haddad, Natalie S.;Haerty, Wilfried;Harris, Rayna M.;Hofmann, Hans A.;Hourlier, Thibaut;Hulata, Gideon;Jaffe, David B.;Lara, Marcia;Lee, Alison P.;MacCallum, Iain;Mwaiko, Salome;Nikaido, Masato;Nishihara, Hidenori;Ozouf-Costaz, Catherine;Penman, David J.;Przybylski, Dariusz;Rakotomanga, Michaelle;Renn, Suzy C. P.;Ribeiro, Filipe J.;Ron, Micha;Salzburger, Walter;Sanchez-Pulido, Luis;Santos, M. Emilia;Searle, Steve;Sharpe, Ted;Swofford, Ross;Tan, Frederick J.;Williams, Louise;Young, Sarah;Yin, Shuangye;Okada, Norihiro;Kocher, Thomas D.;Miska, Eric A.;Lander, Eric S.;Venkatesh, Byrappa;Fernald, Russell D.;Meyer, Axel;Ponting, Chris P.;Streelman, J. Todd;Lindblad-Toh, Kerstin;Seehausen, Ole;Di Palma, Federica
慈鱼以东非五大湖的大型、多样化和重复的适应性辐射而闻名。为了了解慈鱼表型多样性背后的分子机制，我们对非洲五个鱼种谱系的基因组和转录本进行了测序：尼罗罗非鱼是一个低多样性的祖先谱系；东非鱼种的四个成员：Neolamprologus brichardi/Pulcher(较老的辐射，坦噶尼喀湖)，Metriaclima Zebra(最近辐射，马拉维湖)，Pundamilia nyererei(最近辐射，维多利亚湖)和Astatotilapia burtoni(坦噶尼喀湖周围的河流物种)。我们发现，与罗非鱼和其他硬骨鱼相比，东非血统中存在过多的基因复制，大量的非编码元件差异，加速的编码序列进化，与转座元件插入相关的表达差异，以及新的microRNAs的调控。此外，我们分析了来自维多利亚湖的60个个体的序列数据，这些个体代表了六个密切相关的物种，并显示了全基因组在编码和调控变异上的多样化选择，其中一些是从古老的多态中招募的。我们得出的结论是，许多分子机制塑造了东非慈鱼基因组，在放松的净化选择期间积累的标准变异可能对促进随后的进化多样化具有重要意义。
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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影响因子：
64.8
作者：
Jones, Felicity C.;Grabherr, Manfred G.;Chan, Yingguang Frank;Russell, Pamela;Mauceli, Evan;Johnson, Jeremy;Swofford, Ross;Pirun, Mono;Zody, Michael C.;White, Simon;Birney, Ewan;Searle, Stephen;Schmutz, Jeremy;Grimwood, Jane;Dickson, Mark C.;Myers, Richard M.;Miller, Craig T.;Summers, Brian R.;Knecht, Anne K.;Brady, Shannon D.;Zhang, Haili;Pollen, Alex A.;Howes, Timothy;Amemiya, Chris;Lander, Eric S.;Di Palma, Federica;Lindblad-Toh, Kerstin;Kingsley, David M.
通讯作者：
Kingsley, David M.
影响因子：
9.8
作者：
Hofmann CM;O'Quin KE;Marshall NJ;Cronin TW;Seehausen O;Carleton KL
通讯作者：
Carleton KL
影响因子：
10.7
作者：
Loh YH;Bezault E;Muenzel FM;Roberts RB;Swofford R;Barluenga M;Kidd CE;Howe AE;Di Palma F;Lindblad-Toh K;Hey J;Seehausen O;Salzburger W;Kocher TD;Streelman JT
通讯作者：
Streelman JT
影响因子：
56.9
作者：
Lynch, M;Conery, JS
通讯作者：
Conery, JS
影响因子：
10.7
作者：
Genner, Martin J.;Seehausen, Ole;Turner, Georg F.
通讯作者：
Turner, Georg F.