The tuatara genome reveals ancient features of amniote evolution
Neil J. GemmellDepartment of Anatomy, University of Otago, Dunedin, New Zealand. [email protected]Kim RutherfordDepartment of Anatomy, University of Otago, Dunedin, New ZealandStefan ProstLOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, GermanyMarc TollisSchool of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USADavid J. WinterSchool of Fundamental Sciences, Massey University, Palmerston North, New ZealandJonathan R. MaceyPeralta Genomics Institute, Oakland, CA, USADavid L. AdelsonSchool of Biological Sciences, The University of Adelaide, Adelaide, South Australia, AustraliaAlexander SuhDepartment of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, SwedenTerry BertozziEvolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, AustraliaJosé Horacio GrauAmedes Genetics, Amedes Medizinische Dienstleistungen, Berlin, GermanyChris L. OrganDepartment of Earth Sciences, Montana State University, Bozeman, MT, USAPaul P. GardnerDepartment of Biochemistry, University of Otago, Dunedin, New ZealandMatthieu MuffatoEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UKMateus PatrícioEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UKKonstantinos BillisEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UKFergal J. MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UKPaul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UKBent PetersenSection for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DenmarkLin KangEdward Via College of Osteopathic Medicine, Blacksburg, VA, USAPawel MichalakCenter for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USAThomas R. BuckleyManaaki Whenua - Landcare Research, Auckland, New ZealandMelissa A. WilsonSchool of Life Sciences, Arizona State University, Tempe, AZ, USAYuanyuan ChengSchool of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, AustraliaHilary MillerBiomatters, Auckland, New ZealandRyan K. SchottDepartment of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USAMelissa JordanThe New Zealand Institute for Plant and Food Research, Auckland, New ZealandRichard D. NewcombThe New Zealand Institute for Plant and Food Research, Auckland, New ZealandJosé Ignacio ArroyoDepartamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileNicole ValenzuelaDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USATimothy A. HoreDepartment of Anatomy, University of Otago, Dunedin, New ZealandJaime RenartInstituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid, SpainValentina PeonaDepartment of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, SwedenClaire PeartDepartment of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, SwedenVera WarmuthDepartment of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, SwedenLu ZengSchool of Biological Sciences, The University of Adelaide, Adelaide, South Australia, AustraliaR. Daniel KortschakSchool of Biological Sciences, The University of Adelaide, Adelaide, South Australia, AustraliaJoy M RaisonSchool of Biological Sciences, The University of Adelaide, Adelaide, South Australia, AustraliaValeria Velásquez‐ZapataDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USAZhiqiang WuDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USADidac SantesmassesCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, SpainMarco MariottiCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, SpainRoderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, SpainShawn RuppSchool of Life Sciences, Arizona State University, Tempe, AZ, USAVictoria TwortManaaki Whenua - Landcare Research, Auckland, New ZealandNicolás DussexDepartment of Anatomy, University of Otago, Dunedin, New ZealandHelen R. TaylorDepartment of Anatomy, University of Otago, Dunedin, New ZealandHideaki AbeDepartment of Anatomy, University of Otago, Dunedin, New ZealandDonna M. BondDepartment of Anatomy, University of Otago, Dunedin, New ZealandJ. M. PatersonSchool of Biological Sciences, University of Canterbury, Christchurch, New ZealandDaniel G. MulcahyGlobal Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USAVanessa L. GonzálezGlobal Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USACharles G. BarbieriPeralta Genomics Institute, Oakland, CA, USADustin DeMeoPeralta Genomics Institute, Oakland, CA, USAStephan PabingerAustrian Institute of Technology (AIT), Center for Health and Bioresources, Molecular Diagnostics, Vienna, AustriaTracey C. van StijnAgResearch, Invermay Agricultural Centre, Mosgiel, New ZealandShannon ClarkeAgResearch, Invermay Agricultural Centre, Mosgiel, New ZealandOliver A. RyderSan Diego Zoo Institute for Conservation Research, Escondido, CA, USAScott V. EdwardsDepartment of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Cambridge, MA, USASteven L. SalzbergDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USALindsay E. AndersonSchool of Biological Sciences, Victoria University of Wellington, Wellington, New ZealandNicola J. NelsonSchool of Biological Sciences, Victoria University of Wellington, Wellington, New ZealandClive StoneNgatiwai Trust Board, Whangarei, New ZealandNgatiwai Trust BoardNgatiwai Trust Board, Whangarei, New ZealandClive StoneNgatiwai Trust Board, Whangarei, New ZealandJim SmillieNgatiwai Trust Board, Whangarei, New ZealandHaydn EdmondsNgatiwai Trust Board, Whangarei, New Zealand
2020en
ABI
Annotatsiya
Abstract The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . 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 amniotes 2,4 . 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.
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