PUBLICATION

The African coelacanth genome provides insights into tetrapod evolution

Authors
Amemiya, C.T., Alfoldi, J., Lee, A.P., Fan, S., Philippe, H., MacCallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J.J., Robinson, M., Dorrington, R.A., Gerdol, M., Aken, B., Biscotti, M.A., Barucca, M., Baurain, D., Berlin, A.M., Blatch, G.L., Buonocore, F., Burmester, T., Campbell, M.S., Canapa, A., Cannon, J.P., Christoffels, A., de Moro, G., Edkins, A.L., Fan, L., Fausto, A.M., Feiner, N., Forconi, M., Gamieldien, J., Gnerre, S., Gnirke, A., Goldstone, J.V., Haerty, W., Hahn, M.E., Hesse, U., Hoffmann, S., Johnson, J., Karchner, S.I., Karaku, S., Lara, M., Levin, J.Z., Litman, G.W., Mauceli, E., Miyake, T., Mueller, M.G., Nelson, D.R., Nitsche, A., Olmo, E., Ota, T., Pallavicini, A., Panji, S., Picone, B., Ponting, C.P., Prohaska, S.J., Przybylski, D., Saha, N.R., Ravi, V., Ribeiro, F.J., Sauka-Spengler, T., Scapigliati, G., Searle, S.M.J., Sharpe, T., Simakov, O., Stadler, P.F., Stegeman, J.J., Sumiyama, K., Tabbaa, D., Tafer, H., Turner-Maier, J., van Heusden, P., White, S., Williams, L., Yandell, M., Brinkmann, H., Volff, J.N., Tabin, C.J., Shubin, N., Schartl, M., Jaffe, D.B., Postlethwait, J.H., Venkatesh, B., Palma, F.D., Lander, E.S., Meyer, A., and Lindblad-Toh, K.
ID
ZDB-PUB-130417-1
Date
2013
Source
Nature   496: 311-316 (Journal)
Registered Authors
Amemiya, Chris, Braasch, Ingo, Goldstone, Jed, Hahn, Mark E., Karchner, Sibel, Litman, Gary W., Meyer, Axel, Miyake, Tsutomu, Mueller, Gail, Ota, Tatsuya, Postlethwait, John H., Rohner, Nicolas, Saha, Nil Ratan, Schartl, Manfred, Shubin, Neil, Smith, Jeramiah, Stegeman, John J., Venkatesh, Byrappa
Keywords
none
MeSH Terms
  • Animals
  • Animals, Genetically Modified
  • Biological Evolution*
  • Chick Embryo
  • Conserved Sequence/genetics
  • Enhancer Elements, Genetic/genetics
  • Evolution, Molecular
  • Extremities/anatomy & histology
  • Extremities/growth & development
  • Fishes/anatomy & histology
  • Fishes/classification*
  • Fishes/genetics*
  • Fishes/physiology
  • Genes, Homeobox/genetics
  • Genome/genetics*
  • Genomics
  • Immunoglobulin M/genetics
  • Mice
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Vertebrates/anatomy & histology
  • Vertebrates/genetics
  • Vertebrates/physiology
(all 26)
PubMed
23598338 Full text @ Nature
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.

Genes / Markers
Marker Marker Type Name
acvr1lGENEactivin A receptor, type 1 like
and1GENEactinodin1
and2GENEactinodin2
and3GENEactinodin3
and4GENEactinodin4
anxa13GENEannexin A13
anxa13lGENEannexin A13, like
arg2GENEarginase 2
atoh1aGENEatonal bHLH transcription factor 1a
atoh1bGENEatonal bHLH transcription factor 1b
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Figures
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Expression
Phenotype
No data available
Mutations / Transgenics
No data available
Human Disease / Model
No data available
Sequence Targeting Reagents
No data available
Fish
No data available
Antibodies
No data available
Orthology
Engineered Foreign Genes
No data available
Mapping
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Citation
Amemiya, C.T., Alfoldi, J., Lee, A.P., Fan, S., Philippe, H., MacCallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J.J., Robinson, M., Dorrington, R.A., Gerdol, M., Aken, B., Biscotti, M.A., Barucca, M., Baurain, D., Berlin, A.M., Blatch, G.L., Buonocore, F., Burmester, T., Campbell, M.S., Canapa, A., Cannon, J.P., Christoffels, A., de Moro, G., Edkins, A.L., Fan, L., Fausto, A.M., Feiner, N., Forconi, M., Gamieldien, J., Gnerre, S., Gnirke, A., Goldstone, J.V., Haerty, W., Hahn, M.E., Hesse, U., Hoffmann, S., Johnson, J., Karchner, S.I., Karaku, S., Lara, M., Levin, J.Z., Litman, G.W., Mauceli, E., Miyake, T., Mueller, M.G., Nelson, D.R., Nitsche, A., Olmo, E., Ota, T., Pallavicini, A., Panji, S., Picone, B., Ponting, C.P., Prohaska, S.J., Przybylski, D., Saha, N.R., Ravi, V., Ribeiro, F.J., Sauka-Spengler, T., Scapigliati, G., Searle, S.M.J., Sharpe, T., Simakov, O., Stadler, P.F., Stegeman, J.J., Sumiyama, K., Tabbaa, D., Tafer, H., Turner-Maier, J., van Heusden, P., White, S., Williams, L., Yandell, M., Brinkmann, H., Volff, J.N., Tabin, C.J., Shubin, N., Schartl, M., Jaffe, D.B., Postlethwait, J.H., Venkatesh, B., Palma, F.D., Lander, E.S., Meyer, A., and Lindblad-Toh, K. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature. 496:311-316.