The African coelacanth genome provides insights into tetrapod evolution

被引：512

作者：

Amemiya, Chris T. ^{[1
,2
]}

Alfoeldi, Jessica ^{[3
]}

Lee, Alison P. ^{[4
]}

Fan, Shaohua ^{[5
]}

Philippe, Herve ^{[6
]}

MacCallum, Iain ^{[3
]}

Braasch, Ingo ^{[7
]}

Manousaki, Tereza ^{[5
,8
]}

Schneider, Igor ^{[9
]}

Rohner, Nicolas ^{[10
]}

Organ, Chris ^{[11
]}

Chalopin, Domitille ^{[12
]}

Smith, Jeramiah J. ^{[13
]}

Robinson, Mark ^{[1
]}

Dorrington, Rosemary A. ^{[14
]}

Gerdol, Marco ^{[15
]}

Aken, Bronwen ^{[16
]}

Biscotti, Maria Assunta ^{[17
]}

Barucca, Marco ^{[17
]}

Baurain, Denis ^{[18
]}

Berlin, Aaron M. ^{[3
]}

Blatch, Gregory L. ^{[14
,19
]}

Buonocore, Francesco ^{[20
]}

Burmester, Thorsten ^{[21
]}

Campbell, Michael S. ^{[22
]}

Canapa, Adriana ^{[17
]}

Cannon, John P. ^{[23
]}

Christoffels, Alan ^{[24
]}

De Moro, Gianluca ^{[15
]}

Edkins, Adrienne L. ^{[14
]}

Fan, Lin ^{[3
]}

Fausto, Anna Maria ^{[20
]}

Feiner, Nathalie ^{[5
,25
]}

Forconi, Mariko ^{[17
]}

Gamieldien, Junaid ^{[24
]}

Gnerre, Sante ^{[3
]}

Gnirke, Andreas ^{[3
]}

Goldstone, Jared V. ^{[26
]}

Haerty, Wilfried ^{[27
]}

Hahn, Mark E. ^{[26
]}

Hesse, Uljana ^{[24
]}

Hoffmann, Steve ^{[28
]}

Johnson, Jeremy ^{[3
]}

Karchner, Sibel I. ^{[26
]}

Kuraku, Shigehiro ^{[5
]}

Lara, Marcia ^{[3
]}

Levin, Joshua Z. ^{[3
]}

Litman, Gary W. ^{[23
]}

Mauceli, Evan ^{[3
]}

Miyake, Tsutomu ^{[29
]}

机构：

[1] Benaroya Res Inst, Mol Genet Program, Seattle, WA 98101 USA

[2] Univ Washington, Dept Biol, Seattle, WA 98105 USA

[3] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[4] ASTAR, Inst Mol & Cell Biol, Comparat Genom Lab, Singapore 138673, Singapore

[5] Univ Konstanz, Dept Biol, D-78464 Constance, Germany

[6] Univ Montreal, Ctr Robert Cedergren, Dept Biochim, Montreal, PQ H3T 1J4, Canada

[7] Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA

[8] Univ Konstanz, Konstanz Res Sch Chem Biol, D-78464 Constance, Germany

[9] Fed Univ Para, Inst Ciencias Biol, BR-66075110 Belem, Para, Brazil

[10] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[11] Univ Utah, Dept Anthropol, Salt Lake City, UT 84112 USA

[12] Ecole Normale Super Lyon, Inst Genom Fonct Lyon, F-69007 Lyon, France

[13] Univ Kentucky, Dept Biol, Lexington, KY 40506 USA

[14] Rhodes Univ, Dept Biochem Microbiol & Biotechnol, Biomed Biotechnol Res Unit BioBRU, ZA-6139 Grahamstown, South Africa

[15] Univ Trieste, Dept Life Sci, I-34128 Trieste, Italy

[16] Wellcome Trust Sanger Inst, Dept Informat, Hinxton CB10 1SA, S Cambs, England

[17] Polytech Univ Marche, Dept Life & Environm Sci, I-60131 Ancona, Italy

[18] Univ Liege, Dept Life Sci, B-4000 Liege, Belgium

[19] Victoria Univ, Coll Hlth & Biomed, Melbourne, Vic 8001, Australia

[20] Univ Tuscia, Dept Innovat Biol Agrofood & Forest Syst, I-01100 Viterbo, Italy

[21] Univ Hamburg, Dept Biol, D-20146 Hamburg, Germany

[22] Univ Utah, Eccles Inst Human Genet, Salt Lake City, UT 84112 USA

[23] Univ S Florida, Morsani Coll Med, Childrens Res Inst, Dept Pediat, St Petersburg, FL 33701 USA

[24] Univ Western Cape, South African Natl Bioinformat Inst, ZA-7535 Bellville, South Africa

[25] Univ Konstanz, Int Max Planck Res Sch Organismal Biol, D-78464 Constance, Germany

[26] Woods Hole Oceanog Inst, Dept Biol, Woods Hole, MA 02543 USA

[27] Univ Oxford, MRC Funct Genom Unit, Oxford OX1 3PT, England

[28] Univ Leipzig, LIFE Res Ctr Civilizat Dis, Transcriptome Bioinformat Grp, D-04109 Leipzig, Germany

[29] Keio Univ, Grad Sch Sci & Technol, Yokohama, Kanagawa 2238522, Japan

[30] Univ S Florida, All Childrens Hosp, Dept Mol Genet, St Petersburg, FL 33701 USA

[31] Univ Tennessee, Ctr Hlth Sci, Dept Microbiol Immunol & Biochem, Memphis, TN 38163 USA

[32] Univ Leipzig, Dept Comp Sci, Bioinformat Grp, D-04109 Leipzig, Germany

[33] Grad Univ Adv Studies, Dept Evolutionary Studies Biosyst, Hayama 2400193, Japan

[34] Univ Leipzig, Dept Comp Sci, Computat EvoDevo Grp, D-04109 Leipzig, Germany

[35] Univ Oxford, Weatherall Inst Mol Med, Oxford OX1 2JD, England

[36] European Mol Biol Lab, D-69117 Heidelberg, Germany

[37] Natl Inst Genet, Divis Populat Genet, Mishima, Shizuoka 4118540, Japan

[38] Univ Chicago, Chicago, IL 60637 USA

[39] Univ Wurzburg, Dept Physiol Chem, D-97070 Wurzburg, Germany

[40] Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, S-75123 Uppsala, Sweden

来源：

NATURE | 2013年 / 496卷 / 7445期

基金：

英国生物技术与生命科学研究理事会;

关键词：

MITOCHONDRIAL GENOME; LIVING FOSSIL; SEQUENCE; MODEL; GENES; TRANSCRIPTION; CHROMOSOMES; RETENTION; REVEALS; ORIGIN;

D O I：

10.1038/nature12027

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

引用

页码：311 / 316

页数：6

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