Six reference-quality genomes reveal evolution of bat adaptations.

Nature
David JebbEmma C Teeling

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 immun...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 5, 2002·Genome Research·W James Kent
May 28, 2003·Biochemical and Biophysical Research Communications·Wei WangYanggu Shi
Sep 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·W James KentDavid Haussler
May 8, 2004·Science·Gill BejeranoDavid Haussler
Sep 17, 2004·Systematic Biology·Simon Y Ho, Lars Jermiin
Oct 29, 2004·Bioinformatics·Sergei L Kosakovsky PondSpencer V Muse
Dec 21, 2004·Nucleic Acids Research·Huaiyu MiPaul D Thomas
Feb 1, 2005·Science·Emma C TeelingWilliam J Murphy
Dec 24, 2005·Science·Lars S JermiinMichael A Charleston
Mar 18, 2006·Bioinformatics·Tijl De BieMatthew W Hahn
Jun 21, 2006·Proceedings of the National Academy of Sciences of the United States of America·Hidenori NishiharaNorihiro Okada
Aug 24, 2006·Human Molecular Genetics·Johanna VendelinJuha Kere
Mar 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·Aris KatzourakisRobert J Gifford
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Nov 7, 2007·Nature Reviews. Genetics·Thomas WickerAlan H Schulman
Jan 26, 2008·Bioinformatics·Mario StankeDavid Haussler
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Alysha M HeimbergKevin J Peterson
Mar 25, 2009·Bioinformatics·Eric P NawrockiSean R Eddy
Apr 8, 2009·Bioinformatics·György AbrusánWojciech Makalowski
Dec 3, 2010·PLoS Genetics·Aris Katzourakis, Robert J Gifford
Jan 19, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Andrew JohnstonJohann E Gudjonsson
Mar 23, 2011·PLoS Biology·Hervé PhilippeDenis Baurain
Aug 16, 2011·Current Opinion in Immunology·Brianne R BarkerJenny P-Y Ting
Nov 19, 2011·BMC Evolutionary Biology·Derek J TaylorJeremy A Bruenn
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
May 15, 2013·The American Journal of Pathology·Justin TanPhillip I Bird
Jun 12, 2013·Frontiers in Physiology·Gareth JonesStephen J Rossiter
Sep 6, 2013·Nature·Joe ParkerStephen J Rossiter
Nov 5, 2013·Current Biology : CB·Georgia TsagkogeorgaStephen J Rossiter
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alexander HaywardPatric Jern
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Dec 31, 2014·Nature Methods·Jianyi YangYang Zhang
Feb 24, 2015·Molecular Biology and Evolution·Martin D SmithSergei L Kosakovsky Pond
Nov 13, 2015·Bioinformatics·Katharina J HoffMario Stanke
Jan 7, 2016·Genome Biology and Evolution·James E TarverDavide Pisani

❮ Previous
Next ❯

Citations

Aug 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Joana DamasHarris A Lewin
Aug 20, 2020·Nature Reviews. Genetics·Linda Koch
Oct 10, 2020·Science·Daniel G Streicker, Amy T Gilbert
Oct 14, 2020·Molecular Ecology Resources·Megan L PowerEmma C Teeling
Nov 10, 2020·PLoS Biology·Rebekah C Kading, Tigga Kingston
Nov 5, 2020·Environmental Microbiology·Harald Brüssow
Aug 24, 2020·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·D Katterine Bonilla-AldanaAlfonso J Rodriguez-Morales
Feb 11, 2021·Proceedings. Biological Sciences·Louise C AllenJesse R Barber
Feb 13, 2021·Genetics and Molecular Biology·Alexa SadierKaren E Sears
Nov 25, 2020·Annual Review of Animal Biosciences·William J MurphyMark S Springer
Dec 29, 2020·Frontiers in Cellular and Infection Microbiology·Emily Clayton, Muhammad Munir
Jan 22, 2021·Nature·Aaron T IrvingLin-Fa Wang
Mar 7, 2021·Current Biology : CB·Taro NojiriDaisuke Koyabu
Mar 3, 2021·Nature Reviews. Immunology·Lin-Fa WangEmma C Teeling
Mar 9, 2021·Current Opinion in Genetics & Development·Aidan O HowenstineKaren E Sears
Mar 14, 2021·Nature Communications·Gerald S WilkinsonSteve Horvath
Mar 27, 2021·Journal of Biological Rhythms·Brian A UptonRichard A Lang
Mar 5, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Sebastien J PuechmailleNatalie Weber
Apr 4, 2021·Viruses·Ananda Ayyappan Jaguva VasudevanCarsten Münk
Apr 30, 2021·Nature·Constantina TheofanopoulouErich D Jarvis
Jun 4, 2021·Frontiers in Molecular Biosciences·Susanne HoltzeArne Sahm
May 20, 2021·Cell Reports·Peter A LarsonMariano Sanchez-Lockhart
Jul 3, 2021·Biomedicines·James M Harper, Donna J Holmes
Jul 3, 2021·Cells·Zachary W Kockler, Dmitry A Gordenin
Aug 24, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Reyna L GordonNicole Creanza
Aug 14, 2021·Molecular Ecology·Megan L PowerEmma C Teeling
Oct 19, 2021·Frontiers in Immunology·Hao ZhouXinsheng Yao

❮ Previous
Next ❯

Methods Mentioned

BETA
Hi-C
RNA-seq
electrophoresis

Software Mentioned

BUSCO
PAML
est
CESAR
Infernal
HyPhy
BLAST
HISAT2
TASSER
RepeatMasker

Related Concepts

Related Feeds

Auditory Perception

Auditory perception is the ability to receive and interpret information attained by the ears. Here is the latest research on factors and underlying mechanisms that influence auditory perception.

Related Papers

Current Biology : CB
M Brock Fenton, John M Ratcliffe
The Journal of the Arkansas Medical Society
C Mills
Zoonoses and Public Health
M L BakerL-F Wang
Acta Oto-laryngologica
F C ORMEROD, J D PYE
© 2021 Meta ULC. All rights reserved