Six reference-quality genomes reveal evolution of bat adaptations

David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dávalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina K. N. Dechmann, Andrea G. Locatelli, Sébastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller (), Sonja C. Vernes (), Eugene W. Myers () and Emma C. Teeling ()
Additional contact information
David Jebb: Max Planck Institute of Molecular Cell Biology and Genetics
Zixia Huang: University College Dublin
Martin Pippel: Max Planck Institute of Molecular Cell Biology and Genetics
Graham M. Hughes: University College Dublin
Ksenia Lavrichenko: Max Planck Institute for Psycholinguistics
Paolo Devanna: Max Planck Institute for Psycholinguistics
Sylke Winkler: Max Planck Institute of Molecular Cell Biology and Genetics
Lars S. Jermiin: University College Dublin
Emilia C. Skirmuntt: University of Oxford
Aris Katzourakis: University of Oxford
Lucy Burkitt-Gray: University College Dublin
David A. Ray: Texas Tech University
Kevin A. M. Sullivan: Texas Tech University
Juliana G. Roscito: Max Planck Institute of Molecular Cell Biology and Genetics
Bogdan M. Kirilenko: Max Planck Institute of Molecular Cell Biology and Genetics
Liliana M. Dávalos: Stony Brook University
Angelique P. Corthals: John Jay College of Criminal Justice
Megan L. Power: University College Dublin
Gareth Jones: University of Bristol
Roger D. Ransome: University of Bristol
Dina K. N. Dechmann: Max Planck Institute of Animal Behavior
Andrea G. Locatelli: University College Dublin
Sébastien J. Puechmaille: ISEM, University of Montpellier
Olivier Fedrigo: The Rockefeller University
Erich D. Jarvis: The Rockefeller University
Michael Hiller: Max Planck Institute of Molecular Cell Biology and Genetics
Sonja C. Vernes: Max Planck Institute for Psycholinguistics
Eugene W. Myers: Max Planck Institute of Molecular Cell Biology and Genetics
Emma C. Teeling: University College Dublin

Nature, 2020, vol. 583, issue 7817, 578-584

Abstract: 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.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41586-020-2486-3 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:583:y:2020:i:7817:d:10.1038_s41586-020-2486-3

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-020-2486-3

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().