The tuatara genome reveals ancient features of amniote evolution

Neil J. Gemmell (), Kim Rutherford, Stefan Prost, Marc Tollis, David Winter, J. Robert Macey, David L. Adelson, Alexander Suh, Terry Bertozzi, José H. Grau, Chris Organ, Paul P. Gardner, Matthieu Muffato, Mateus Patricio, Konstantinos Billis, Fergal J. Martin, Paul Flicek, Bent Petersen, Lin Kang, Pawel Michalak, Thomas R. Buckley, Melissa Wilson, Yuanyuan Cheng, Hilary Miller, Ryan K. Schott, Melissa D. Jordan, Richard D. Newcomb, José Ignacio Arroyo, Nicole Valenzuela, Tim A. Hore, Jaime Renart, Valentina Peona, Claire R. Peart, Vera M. Warmuth, Lu Zeng, R. Daniel Kortschak, Joy M. Raison, Valeria Velásquez Zapata, Zhiqiang Wu, Didac Santesmasses, Marco Mariotti, Roderic Guigó, Shawn M. Rupp, Victoria G. Twort, Nicolas Dussex, Helen Taylor, Hideaki Abe, Donna M. Bond, James M. Paterson, Daniel G. Mulcahy, Vanessa L. Gonzalez, Charles G. Barbieri, Dustin P. DeMeo, Stephan Pabinger, Tracey Stijn, Shannon Clarke, Oliver Ryder, Scott V. Edwards, Steven L. Salzberg, Lindsay Anderson, Nicola Nelson and Clive Stone
Additional contact information
Neil J. Gemmell: University of Otago
Kim Rutherford: University of Otago
Stefan Prost: Senckenberg Museum
Marc Tollis: Arizona State University
David Winter: Massey University
J. Robert Macey: Peralta Genomics Institute
David L. Adelson: The University of Adelaide
Alexander Suh: Uppsala University
Terry Bertozzi: The University of Adelaide
José H. Grau: Amedes Medizinische Dienstleistungen
Chris Organ: Montana State University
Paul P. Gardner: University of Otago
Matthieu Muffato: European Bioinformatics Institute
Mateus Patricio: European Bioinformatics Institute
Konstantinos Billis: European Bioinformatics Institute
Fergal J. Martin: European Bioinformatics Institute
Paul Flicek: European Bioinformatics Institute
Bent Petersen: University of Copenhagen
Lin Kang: Edward Via College of Osteopathic Medicine
Pawel Michalak: Edward Via College of Osteopathic Medicine
Thomas R. Buckley: Manaaki Whenua - Landcare Research
Melissa Wilson: Arizona State University
Yuanyuan Cheng: The University of Sydney
Hilary Miller: Biomatters
Ryan K. Schott: National Museum of Natural History, Smithsonian Institution
Melissa D. Jordan: The New Zealand Institute for Plant and Food Research
Richard D. Newcomb: The New Zealand Institute for Plant and Food Research
José Ignacio Arroyo: Pontificia Universidad Católica de Chile
Nicole Valenzuela: Iowa State University
Tim A. Hore: University of Otago
Jaime Renart: Instituto de Investigaciones Biomédicas ‘Alberto Sols’ CSIC-UAM
Valentina Peona: Uppsala University
Claire R. Peart: Uppsala University
Vera M. Warmuth: Uppsala University
Lu Zeng: The University of Adelaide
R. Daniel Kortschak: The University of Adelaide
Joy M. Raison: The University of Adelaide
Valeria Velásquez Zapata: Iowa State University
Zhiqiang Wu: Iowa State University
Didac Santesmasses: Universitat Pompeu Fabra (UPF)
Marco Mariotti: Universitat Pompeu Fabra (UPF)
Roderic Guigó: Universitat Pompeu Fabra (UPF)
Shawn M. Rupp: Arizona State University
Victoria G. Twort: Manaaki Whenua - Landcare Research
Nicolas Dussex: University of Otago
Helen Taylor: University of Otago
Hideaki Abe: University of Otago
Donna M. Bond: University of Otago
James M. Paterson: University of Canterbury
Daniel G. Mulcahy: National Museum of Natural History, Smithsonian Institution
Vanessa L. Gonzalez: National Museum of Natural History, Smithsonian Institution
Charles G. Barbieri: Peralta Genomics Institute
Dustin P. DeMeo: Peralta Genomics Institute
Stephan Pabinger: Center for Health and Bioresources, Molecular Diagnostics
Tracey Stijn: AgResearch, Invermay Agricultural Centre
Shannon Clarke: AgResearch, Invermay Agricultural Centre
Oliver Ryder: San Diego Zoo Institute for Conservation Research
Scott V. Edwards: Harvard University
Steven L. Salzberg: Johns Hopkins University
Lindsay Anderson: Victoria University of Wellington
Nicola Nelson: Victoria University of Wellington
Clive Stone: Ngatiwai Trust Board

Nature, 2020, vol. 584, issue 7821, 403-409

Abstract: Abstract The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.

Date: 2020
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DOI: 10.1038/s41586-020-2561-9

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