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 ORCID: https://orcid.org/0000-0003-0111-191X, 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 and Lindblad-Toh, Kerstin (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature, 496 (7445). pp. 311-316. ISSN 0028-0836

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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.

Item Type: Article
Additional Information: 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.
Uncontrolled Keywords: general ,/dk/atira/pure/subjectarea/asjc/1000
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 15 Sep 2022 14:30
Last Modified: 30 Sep 2022 02:36
URI: https://ueaeprints.uea.ac.uk/id/eprint/88332
DOI: 10.1038/nature12027

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