Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.

Autor: Yu D; Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; University of Chinese Academy of Sciences, Beijing, China., Ren Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China., Uesaka M; Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.; Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan., Beavan AJS; Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.; School of Life Sciences, University of Nottingham, Nottingham, UK., Muffato M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.; Tree of Life, Wellcome Sanger Institute, Hinxton, UK., Shen J; Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.; University of Chinese Academy of Sciences, Beijing, China., Li Y; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China., Sato I; Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.; iPS Cell Advanced Characterization and Development Team, RIKEN BioResource Research Center, Tsukuba, Japan., Wan W; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China., Clark JW; Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.; Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK., Keating JN; Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK., Carlisle EM; Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK., Dearden RP; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.; Naturalis Biodiversity Center, Leiden, the Netherlands., Giles S; School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK., Randle E; Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK., Sansom RS; Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK., Feuda R; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK., Fleming JF; Keio University Institute for Advanced Biosciences, Tsuruoka, Japan.; Natural History Museum, University of Oslo, Oslo, Norway., Sugahara F; Division of Biology, Hyogo Medical University, Nishinomiya, Japan.; Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan., Cummins C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK., Patricio M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK., Akanni W; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK., D'Aniello S; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy., Bertolucci C; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy.; Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy., Irie N; Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan., Alev C; Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan., Sheng G; International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan., de Mendoza A; School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK., Maeso I; Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain.; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain., Irimia M; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.; ICREA, Barcelona, Spain., Fromm B; The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway., Peterson KJ; Department of Biological Sciences, Dartmouth College, Hanover, NH, USA., Das S; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.; Emory Vaccine Center, Emory University, Atlanta, GA, USA., Hirano M; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.; Emory Vaccine Center, Emory University, Atlanta, GA, USA., Rast JP; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.; Emory Vaccine Center, Emory University, Atlanta, GA, USA., Cooper MD; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.; Emory Vaccine Center, Emory University, Atlanta, GA, USA., Paps J; Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK., Pisani D; Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.; Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK., Kuratani S; Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.; Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan., Martin FJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK. fergal@ebi.ac.uk., Wang W; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. wwang@mail.kiz.ac.cn.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China. wwang@mail.kiz.ac.cn.; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. wwang@mail.kiz.ac.cn., Donoghue PCJ; Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK. Phil.Donoghue@bristol.ac.uk., Zhang YE; Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. zhangyong@ioz.ac.cn.; University of Chinese Academy of Sciences, Beijing, China. zhangyong@ioz.ac.cn.; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. zhangyong@ioz.ac.cn., Pascual-Anaya J; Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan. jpascualanaya@gmail.com.; Department of Animal Biology, Faculty of Science, University of Málaga (UMA), Málaga, Spain. jpascualanaya@gmail.com.; Edificio de Bioinnovación, Universidad de Málaga, Málaga, Spain. jpascualanaya@gmail.com.
Jazyk: angličtina
Zdroj: Nature ecology & evolution [Nat Ecol Evol] 2024 Mar; Vol. 8 (3), pp. 519-535. Date of Electronic Publication: 2024 Jan 12.
DOI: 10.1038/s41559-023-02299-z
Abstrakt: Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.
(© 2024. The Author(s).)
Databáze: MEDLINE
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