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.
| Original language | English |
|---|---|
| Pages (from-to) | 311-316 |
| Number of pages | 6 |
| Journal | Nature |
| Volume | 496 |
| Issue number | 7445 |
| DOIs | |
| Publication status | Published - 18 Apr 2013 |
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The African coelacanth genome provides insights into tetrapod evolution. / Amemiya, Chris T.; Alfoldi, Jessica; Lee, Alison P.; Fan, Shaohua; Philippe, Hervé; MacCallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor; Rohner, Nicolas; Organ, Chris; Chalopin, Domitille; Smith, Jeramiah J.; Robinson, Mark; Dorrington, Rosemary A.; Gerdol, Marco; Aken, Bronwen; Biscotti, Maria Assunta; Barucca, Marco; Baurain, Denis; Berlin, Aaron M.; Blatch, Gregory L.; Buonocore, Francesco; Burmester, Thorsten; Campbell, Michael S.; Canapa, Adriana; Cannon, John P.; Christoffels, Alan; De Moro, Gianluca; Edkins, Adrienne L.; Fan, Lin; Fausto, Anna Maria; Feiner, Nathalie; Forconi, Mariko; Gamieldien, Junaid; Gnerre, Sante; Gnirke, Andreas; Goldstone, Jared V.; Haerty, Wilfried; Hahn, Mark E.; Hesse, Uljana; Hoffmann, Steve; Johnson, Jeremy; Karchner, Sibel I.; Kuraku, Shigehiro; Lara, Marcia; Levin, Joshua Z.; Litman, Gary W.; Mauceli, Evan; Miyake, Tsutomu; Mueller, M. Gail; Nelson, David R.; Nitsche, Anne; Olmo, Ettore; Ota, Tatsuya; Pallavicini, Alberto; Panji, Sumir; Picone, Barbara; Ponting, Chris P.; Prohaska, Sonja J.; Przybylski, Dariusz; Saha, Nil Ratan; Ravi, Vydianathan; Ribeiro, Filipe J.; Sauka-Spengler, Tatjana; Scapigliati, Giuseppe; Searle, Stephen M.J.; Sharpe, Ted; Simakov, Oleg; Stadler, Peter F.; Stegeman, John J.; Sumiyama, Kenta; Tabbaa, Diana; Tafer, Hakim; Turner-Maier, Jason; Van Heusden, Peter; White, Simon; Williams, Louise; Yandell, Mark; Brinkmann, Henner; Volff, Jean Nicolas; Tabin, Clifford J.; Shubin, Neil; Schartl, Manfred; Jaffe, David B.; Postlethwait, John H.; Venkatesh, Byrappa; Di Palma, Federica; Lander, Eric S.; Meyer, Axel; Lindblad-Toh, Kerstin.
In: Nature, Vol. 496, No. 7445, 18.04.2013, p. 311-316.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - The African coelacanth genome provides insights into tetrapod evolution
AU - Amemiya, Chris T.
AU - Alfoldi, Jessica
AU - Lee, Alison P.
AU - Fan, Shaohua
AU - Philippe, Hervé
AU - MacCallum, Iain
AU - Braasch, Ingo
AU - Manousaki, Tereza
AU - Schneider, Igor
AU - Rohner, Nicolas
AU - Organ, Chris
AU - Chalopin, Domitille
AU - Smith, Jeramiah J.
AU - Robinson, Mark
AU - Dorrington, Rosemary A.
AU - Gerdol, Marco
AU - Aken, Bronwen
AU - Biscotti, Maria Assunta
AU - Barucca, Marco
AU - Baurain, Denis
AU - Berlin, Aaron M.
AU - Blatch, Gregory L.
AU - Buonocore, Francesco
AU - Burmester, Thorsten
AU - Campbell, Michael S.
AU - Canapa, Adriana
AU - Cannon, John P.
AU - Christoffels, Alan
AU - De Moro, Gianluca
AU - Edkins, Adrienne L.
AU - Fan, Lin
AU - Fausto, Anna Maria
AU - Feiner, Nathalie
AU - Forconi, Mariko
AU - Gamieldien, Junaid
AU - Gnerre, Sante
AU - Gnirke, Andreas
AU - Goldstone, Jared V.
AU - Haerty, Wilfried
AU - Hahn, Mark E.
AU - Hesse, Uljana
AU - Hoffmann, Steve
AU - Johnson, Jeremy
AU - Karchner, Sibel I.
AU - Kuraku, Shigehiro
AU - Lara, Marcia
AU - Levin, Joshua Z.
AU - Litman, Gary W.
AU - Mauceli, Evan
AU - Miyake, Tsutomu
AU - Mueller, M. Gail
AU - Nelson, David R.
AU - Nitsche, Anne
AU - Olmo, Ettore
AU - Ota, Tatsuya
AU - Pallavicini, Alberto
AU - Panji, Sumir
AU - Picone, Barbara
AU - Ponting, Chris P.
AU - Prohaska, Sonja J.
AU - Przybylski, Dariusz
AU - Saha, Nil Ratan
AU - Ravi, Vydianathan
AU - Ribeiro, Filipe J.
AU - Sauka-Spengler, Tatjana
AU - Scapigliati, Giuseppe
AU - Searle, Stephen M.J.
AU - Sharpe, Ted
AU - Simakov, Oleg
AU - Stadler, Peter F.
AU - Stegeman, John J.
AU - Sumiyama, Kenta
AU - Tabbaa, Diana
AU - Tafer, Hakim
AU - Turner-Maier, Jason
AU - Van Heusden, Peter
AU - White, Simon
AU - Williams, Louise
AU - Yandell, Mark
AU - Brinkmann, Henner
AU - Volff, Jean Nicolas
AU - Tabin, Clifford J.
AU - Shubin, Neil
AU - Schartl, Manfred
AU - Jaffe, David B.
AU - Postlethwait, John H.
AU - Venkatesh, Byrappa
AU - Di Palma, Federica
AU - Lander, Eric S.
AU - Meyer, Axel
AU - Lindblad-Toh, Kerstin
N1 - Funding Information: Acknowledgements Acquisition and storage of Latimeria chalumnae samples was supported by grants from the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology. Generation of the Latimeria chalumnae and Protopterus annectens sequences by the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University was supported by grants from the National Human Genome Research Institute (NHGRI). K.L.T. is the recipient of a EURYI award from the European Science Foundation. We would also like to thank the Genomics Sequencing Platform of the Broad Institute for sequencing the L. chalumnae genome and L. chalumnae and P. annectens transcriptomes, S. Ahamada, R. Stobbs and the Association pour le Protection de Gombesa (APG) for their help in obtaining coelacanth samples, Y. Zhao for the use of data from Rana chensinensis, and L. Gaffney, C. Hamilton and J. Westlund for assistance with figure preparation.
PY - 2013/4/18
Y1 - 2013/4/18
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84876271982&partnerID=8YFLogxK
U2 - 10.1038/nature12027
DO - 10.1038/nature12027
M3 - Article
C2 - 23598338
AN - SCOPUS:84876271982
VL - 496
SP - 311
EP - 316
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7445
ER -