Six reference-quality genomes reveal evolution of bat adaptations.

Autor: Jebb D; 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., Huang Z; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland., Pippel M; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.; Center for Systems Biology Dresden, Dresden, Germany., Hughes GM; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland., Lavrichenko K; Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands., Devanna P; Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands., Winkler S; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Jermiin LS; 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., Skirmuntt EC; Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, UK., Katzourakis A; Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Oxford, UK., Burkitt-Gray L; Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland., Ray DA; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA., Sullivan KAM; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA., Roscito JG; 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., Kirilenko BM; 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., Dávalos LM; 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., Corthals AP; Department of Sciences, John Jay College of Criminal Justice, New York, NY, USA., Power ML; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland., Jones G; School of Biological Sciences, University of Bristol, Bristol, UK., Ransome RD; School of Biological Sciences, University of Bristol, Bristol, UK., Dechmann DKN; 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., Locatelli AG; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland., Puechmaille SJ; ISEM, University of Montpellier, Montpellier, France.; Zoological Institute and Museum, University of Greifswald, Greifswald, Germany., Fedrigo O; Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA., Jarvis ED; 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., Hiller M; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. hiller@mpi-cbg.de.; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany. hiller@mpi-cbg.de.; Center for Systems Biology Dresden, Dresden, Germany. hiller@mpi-cbg.de., Vernes SC; Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands. sonja.vernes@mpi.nl.; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands. sonja.vernes@mpi.nl., Myers EW; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. gene@mpi-cbg.de.; Center for Systems Biology Dresden, Dresden, Germany. gene@mpi-cbg.de.; Faculty of Computer Science, Technical University Dresden, Dresden, Germany. gene@mpi-cbg.de., Teeling EC; School of Biology and Environmental Science, University College Dublin, Dublin, Ireland. emma.teeling@ucd.ie.
Jazyk: angličtina
Zdroj: Nature [Nature] 2020 Jul; Vol. 583 (7817), pp. 578-584. Date of Electronic Publication: 2020 Jul 22.
DOI: 10.1038/s41586-020-2486-3
Abstrakt: 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 protocols 1 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 disease 1 .
Databáze: MEDLINE
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