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The African coelacanth genome provides insights into tetrapod evolution

Amemiya, Chris T; Alföldi, Jessica; Lee, Alison P; Fan, Shaohua; Philippe, Hervé; Maccallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor and Rohner, Nicolas, et al. (2013) In Nature 496(7445). p.311-316
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... (More)

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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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
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Nature
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496
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7445
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311 - 316
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Nature Publishing Group
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  • scopus:84876271982
ISSN
0028-0836
DOI
10.1038/nature12027
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English
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ff6240dc-3807-471f-9cf9-eb86285c32a0
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@article{ff6240dc-3807-471f-9cf9-eb86285c32a0,
  abstract     = {<p>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.</p>},
  author       = {Amemiya, Chris T and Alföldi, Jessica and Lee, Alison P and Fan, Shaohua and Philippe, Hervé and Maccallum, Iain and Braasch, Ingo and Manousaki, Tereza and Schneider, Igor and Rohner, Nicolas and Organ, Chris and Chalopin, Domitille and Smith, Jeramiah J and Robinson, Mark and Dorrington, Rosemary A and Gerdol, Marco and Aken, Bronwen and Biscotti, Maria Assunta and Barucca, Marco and Baurain, Denis and Berlin, Aaron M and Blatch, Gregory L and Buonocore, Francesco and Burmester, Thorsten and Campbell, Michael S and Canapa, Adriana and Cannon, John P and Christoffels, Alan and De Moro, Gianluca and Edkins, Adrienne L and Fan, Lin and Fausto, Anna Maria and Feiner, Nathalie and Forconi, Mariko and Gamieldien, Junaid and Gnerre, Sante and Gnirke, Andreas and Goldstone, Jared V and Haerty, Wilfried and Hahn, Mark E and Hesse, Uljana and Hoffmann, Steve and Johnson, Jeremy and Karchner, Sibel I and Kuraku, Shigehiro and Lara, Marcia and Levin, Joshua Z and Litman, Gary W and Mauceli, Evan and Miyake, Tsutomu and Mueller, M Gail and Nelson, David R and Nitsche, Anne and Olmo, Ettore and Ota, Tatsuya and Pallavicini, Alberto and Panji, Sumir and Picone, Barbara and Ponting, Chris P and Prohaska, Sonja J and Przybylski, Dariusz and Saha, Nil Ratan and Ravi, Vydianathan and Ribeiro, Filipe J and Sauka-Spengler, Tatjana and Scapigliati, Giuseppe and Searle, Stephen M J and Sharpe, Ted and Simakov, Oleg and Stadler, Peter F and Stegeman, John J and Sumiyama, Kenta and Tabbaa, Diana and Tafer, Hakim and Turner-Maier, Jason and van Heusden, Peter and White, Simon and Williams, Louise and Yandell, Mark and Brinkmann, Henner and Volff, Jean-Nicolas and Tabin, Clifford J and Shubin, Neil and Schartl, Manfred and Jaffe, David B and Postlethwait, John H and Venkatesh, Byrappa and Di Palma, Federica and Lander, Eric S and Meyer, Axel and Lindblad-Toh, Kerstin},
  issn         = {0028-0836},
  keyword      = {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},
  language     = {eng},
  month        = {04},
  number       = {7445},
  pages        = {311--316},
  publisher    = {Nature Publishing Group},
  series       = {Nature},
  title        = {The African coelacanth genome provides insights into tetrapod evolution},
  url          = {http://dx.doi.org/10.1038/nature12027},
  volume       = {496},
  year         = {2013},
}