The African coelacanth genome provides insights into tetrapod evolution

Research output: Contribution to journalArticle

Abstract

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.

Details

Authors
  • Chris T Amemiya
  • Jessica Alföldi
  • Alison P Lee
  • Shaohua Fan
  • Hervé 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
  • 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
External organisations
  • Benaroya Research Institute
  • University of Konstanz
  • University of Washington, Seattle
  • Broad Institute
  • A*Star Institute of Molecular and Cell Biology (IMCB)
  • University of Montreal, Canada
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Evolutionary Biology
  • Zoology

Keywords

  • Animals, Animals, Genetically Modified, Biological Evolution, Chick Embryo, Conserved Sequence, Enhancer Elements, Genetic, Evolution, Molecular, Extremities, Fishes, Genes, Homeobox, Genome, Genomics, Immunoglobulin M, Mice, Molecular Sequence Annotation, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, DNA, Vertebrates, Journal Article, Research Support, Non-U.S. Gov't
Original languageEnglish
Pages (from-to)311-316
JournalNature
Volume496
Issue number7445
Publication statusPublished - 2013 Apr 18
Publication categoryResearch
Peer-reviewedYes
Externally publishedYes