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Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann DKN, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M, Vernes SC, Myers EW, Teeling EC. Six reference-quality genomes reveal evolution of bat adaptations. Nature 2020; 583:578-584. [PMID: 32699395 PMCID: PMC8075899 DOI: 10.1038/s41586-020-2486-3] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 06/09/2020] [Indexed: 11/08/2022]
Abstract
Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our 'Tool to infer Orthologs from Genome Alignments' (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.
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Affiliation(s)
- David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Ksenia Lavrichenko
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lars S Jermiin
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Earth Institute, University College Dublin, Dublin, Ireland
| | - Emilia C Skirmuntt
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, UK
| | - Aris Katzourakis
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, UK
| | - Lucy Burkitt-Gray
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Kevin A M Sullivan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Bogdan M Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | | | - Megan L Power
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Roger D Ransome
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Dina K N Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Andrea G Locatelli
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Sébastien J Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Olivier Fedrigo
- Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
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