The African coelacanth genome provides insights into tetrapod evolution

Chris T Amemiya; Jessica Alföldi; Alison P Lee; Shaohua Fan; Herve Philippe; Iain Maccallum; Ingo Braasch; Tereza Manousaki; Igor Schneider; Nicolas Rohner; Chris Organ; Domitille Chalopin; Jeramiah J Smith; Mark Robinson; Rosemary A Dorrington; Marco Gerdol; Bronwen Aken; Maria Assunta Biscotti; Marco Barucca; Denis Baurain; Aaron M Berlin; Gregory L Blatch; Francesco Buonocore; Thorsten Burmester; Michael S Campbell; Adriana Canapa; John P Cannon; Alan Christoffels; Gianluca De Moro; Adrienne L Edkins; Lin Fan; Anna Maria Fausto; Nathalie Feiner; Mariko Forconi; Junaid Gamieldien; Sante Gnerre; Andreas Gnirke; Jared V Goldstone; Wilfried Haerty; Mark E Hahn; Uljana Hesse; Steve Hoffmann; Jeremy Johnson; Sibel I Karchner; Shigehiro Kuraku; Marcia Lara; Joshua Z Levin; Gary W Litman; Evan Mauceli; Tsutomu Miyake; M Gail Mueller; David R Nelson; Anne Nitsche; Ettore Olmo; Tatsuya Ota; Alberto Pallavicini; Sumir Panji; Barbara Picone; Chris P Ponting; Sonja J Prohaska; Dariusz Przybylski; Nil Ratan Saha; Vydianathan Ravi; Filipe J Ribeiro; Tatjana Sauka-Spengler; Giuseppe Scapigliati; Stephen M. J Searle; Ted Sharpe; Oleg Simakov; Peter F Stadler; John J Stegeman; Kenta Sumiyama; Diana Tabbaa; Hakim Tafer; Jason Turner-Maier; Peter van Heusden; Simon White; Louise Williams; Mark Yandell; Henner Brinkmann; Jean-Nicolas Volff; Clifford J Tabin; Neil Shubin; Manfred Schartl; David B Jaffe; John H Postlethwait; Byrappa Venkatesh; Federica Di Palma; Eric S Lander; Axel Meyer; Kerstin Lindblad-Toh

doi:10.1038/nature12027

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The African coelacanth genome provides insights into tetrapod evolution

Journal article

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The African coelacanth genome provides insights into tetrapod evolution

Chris T Amemiya, Jessica Alföldi, Alison P Lee, Shaohua Fan, Herve Philippe, Iain Maccallum, Ingo Braasch, Tereza Manousaki, Igor Schneider, Nicolas Rohner, …

Nature, Vol.496(7445), pp.311-316

04/17/2013

DOI: https://doi.org/10.1038/nature12027

PMID: 23598338

Abstract

Comparative genomics

Genome evolution

Life Sciences

Computer Science

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.

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Title: The African coelacanth genome provides insights into tetrapod evolution
Creators: Chris T Amemiya - Molecular Genetics Program
Jessica Alföldi - Broad Institute of MIT and Harvard
Alison P Lee - Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, ASTAR, Biopolis
Shaohua Fan - Department of Biology
Herve Philippe - Université de Montréal
Iain Maccallum - Broad Institute of MIT and Harvard
Ingo Braasch - Institute of Neuroscience
Tereza Manousaki - Department of Biology
Igor Schneider - Instituto de Ciências Biológicas
Nicolas Rohner - Department of Genetics [Boston]
Chris Organ - Utah State University
Domitille Chalopin - Institut de Génomique Fonctionnelle de Lyon
Jeramiah J Smith - Department of Biology
Mark Robinson - Molecular Genetics Program
Rosemary A Dorrington - Rhodes University, Grahamstown
Marco Gerdol - Department of Life Sciences
Bronwen Aken - Wellcome Trust Sanger Institute
Maria Assunta Biscotti - Università Politecnica delle Marche [Ancona]
Marco Barucca - Università Politecnica delle Marche [Ancona]
Denis Baurain - Université de Liège
Aaron M Berlin - Broad Institute of MIT and Harvard
Gregory L Blatch - Rhodes University, Grahamstown
Francesco Buonocore - Department for Innovation in Biological, Agro-Food and Forest Systems
Thorsten Burmester - University of Hamburg
Michael S Campbell - Eccles Institute of Human Genetics
Adriana Canapa - Università Politecnica delle Marche [Ancona]
John P Cannon - University of South Florida [Tampa]
Alan Christoffels - South African National Bioinformatics Institute
Gianluca De Moro - Department of Life Sciences
Adrienne L Edkins - Rhodes University, Grahamstown
Lin Fan - Broad Institute of MIT and Harvard
Anna Maria Fausto - Department for Innovation in Biological, Agro-Food and Forest Systems
Nathalie Feiner - Department of Biology
Mariko Forconi - Università Politecnica delle Marche [Ancona]
Junaid Gamieldien - South African National Bioinformatics Institute
Sante Gnerre - Broad Institute of MIT and Harvard
Andreas Gnirke - Broad Institute of MIT and Harvard
Jared V Goldstone - Biology Department
Wilfried Haerty - University of Oxford [Oxford]
Mark E Hahn - Biology Department
Uljana Hesse - South African National Bioinformatics Institute
Steve Hoffmann - Leipzig University
Jeremy Johnson - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Sibel I Karchner - Biology Department
Shigehiro Kuraku - Department of Biology
Marcia Lara - Broad Institute of MIT and Harvard
Joshua Z Levin - Broad Institute of MIT and Harvard
Gary W Litman - University of South Florida [Tampa]
Evan Mauceli - Broad Institute of MIT and Harvard
Tsutomu Miyake - Keio University
M Gail Mueller - All Children’s Hospital
David R Nelson - University of Tennessee
Anne Nitsche - Bioinformatics Group, Department of Computer Science
Ettore Olmo - Università Politecnica delle Marche [Ancona]
Tatsuya Ota - Graduate University for Advanced Studies
Alberto Pallavicini - Department of Life Sciences
Sumir Panji - South African National Bioinformatics Institute
Barbara Picone - South African National Bioinformatics Institute
Chris P Ponting - University of Oxford [Oxford]
Sonja J Prohaska - Leipzig University
Dariusz Przybylski - Broad Institute of MIT and Harvard
Nil Ratan Saha - Molecular Genetics Program
Vydianathan Ravi - Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, ASTAR, Biopolis, Singapore 138673, Singapore
Filipe J Ribeiro - Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Tatjana Sauka-Spengler - University of Oxford [Oxford]
Giuseppe Scapigliati - Department for Innovation in Biological, Agro-Food and Forest Systems
Stephen M. J Searle - Wellcome Trust Sanger Institute
Ted Sharpe - Broad Institute of MIT and Harvard
Oleg Simakov - Department of Biology
Peter F Stadler - Bioinformatics Group, Department of Computer Science
John J Stegeman - Biology Department
Kenta Sumiyama - National Institute of Genetics
Diana Tabbaa - Broad Institute of MIT and Harvard
Hakim Tafer - Bioinformatics Group, Department of Computer Science
Jason Turner-Maier - Broad Institute of MIT and Harvard
Peter van Heusden - South African National Bioinformatics Institute
Simon White - Wellcome Trust Sanger Institute
Louise Williams - Broad Institute of MIT and Harvard
Mark Yandell - Eccles Institute of Human Genetics
Henner Brinkmann - Université de Montréal
Jean-Nicolas Volff - Institut de Génomique Fonctionnelle de Lyon
Clifford J Tabin - Department of Genetics [Boston]
Neil Shubin - University of Chicago
Manfred Schartl - Department Physiological Chemistry, Biocenter
David B Jaffe - Broad Institute of MIT and Harvard
John H Postlethwait - Institute of Neuroscience
Byrappa Venkatesh - Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, ASTAR, Biopolis
Federica Di Palma - Broad Institute of MIT and Harvard
Eric S Lander - Broad Institute of MIT and Harvard
Axel Meyer - Department of Biology
Kerstin Lindblad-Toh - Broad Institute of MIT and Harvard
Publication Details: Nature, Vol.496(7445), pp.311-316
Publisher: Nature Publishing Group
Identifiers: 9924012911001921
Academic Unit: Department of Biology
Language: English
Resource Type: Journal article

The African coelacanth genome provides insights into tetrapod evolution

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