The genome of a songbird

Wesley C. Warren; David F. Clayton; Hans Ellegren; Arthur P. Arnold; LaDeana W. Hillier; Axel Kuenstner; Steve Searle; Simon White; Albert J. Vilella; Susan Fairley; Andreas Heger; Lesheng Kong; Chris P. Ponting; Erich D. Jarvis; Claudio V. Mello; Pat Minx; Peter Lovell; Tarciso A. F. Velho; Margaret Ferris; Christopher N. Balakrishnan; Saurabh Sinha; Charles Blatti; Sarah E. London; Yun Li; Ya-Chi Lin; Julia George; Jonathan Sweedler; Bruce Southey; Preethi Gunaratne; Michael Watson; Kiwoong Nam; Niclas Backstroem; Linnea Smeds; Benoit Nabholz; Yuichiro Itoh; Osceola Whitney; Andreas R. Pfenning; Jason Howard; Martin Voelker; Bejamin M. Skinner; Darren K. Griffin; Liang Ye; William M. McLaren; Paul Flicek; Victor Quesada; Gloria Velasco; Carlos Lopez-Otin; Xose S. Puente; Tsviya Olender; Doron Lancet; Arian F. A. Smit; Robert Hubley; Miriam K. Konkel; Jerilyn A. Walker; Mark A. Batzer; Wanjun Gu; David D. Pollock; Lin Chen; Ze Cheng; Evan E. Eichler; Jessica Stapley; Jon Slate; Robert Ekblom; Tim Birkhead; Terry Burke; David Burt; Constance Scharff; Iris Adam; Hugues Richard; Marc Sultan; Alexey Soldatov; Hans Lehrach; Scott V. Edwards; Shiaw-Pyng Yang; XiaoChing Li; Tina Graves; Lucinda Fulton; Joanne Nelson; Asif Chinwalla; Shunfeng Hou; Elaine R. Mardis; Richard K. Wilson

doi:10.1038/nature08819

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The genome of a songbird

Wesley C. Warren, David F. Clayton, Hans Ellegren, Arthur P. Arnold, LaDeana W. Hillier, Axel Kuenstner, Steve Searle, Simon White, Albert J. Vilella, Susan Fairley, …

Nature (London), Vol.464(7289), pp.757-762

01/04/2010

DOI: https://doi.org/10.1038/nature08819

PMID: 20360741

Résumé

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

The zebra finch is an important model organism in several fields(1,2) with unique relevance to human neuroscience(3,4). Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken(5)-the only bird with a sequenced genome until now(6). Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes(7). We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.

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Détails

Titre: The genome of a songbird
Créateurs - sans rôle: Wesley C. Warren - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
David F. Clayton - Univ Illinois, Urbana, IL 61801 USA
Hans Ellegren - Uppsala University
Arthur P. Arnold - Univ Calif Los Angeles, Los Angeles, CA 90056 USA
LaDeana W. Hillier - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Axel Kuenstner - Uppsala Univ, Inst Evolut & Genet Syst, S-75236 Uppsala, Sweden
Steve Searle - Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
Simon White - Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
Albert J. Vilella - EMBL EBI, Cambridge CB10 1SD, England
Susan Fairley - Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
Andreas Heger - Univ Oxford, Funct Genom Unit, MRC, Dept Physiol Anat & Genet, Oxford OX1 3QX, England
Lesheng Kong - Univ Oxford, Funct Genom Unit, MRC, Dept Physiol Anat & Genet, Oxford OX1 3QX, England
Chris P. Ponting - Univ Oxford, Funct Genom Unit, MRC, Dept Physiol Anat & Genet, Oxford OX1 3QX, England
Erich D. Jarvis - Duke University
Claudio V. Mello - University of Portland
Pat Minx - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Peter Lovell - University of Portland
Tarciso A. F. Velho - Oregon Hlth & Sci Univ, Dept Behav Neurosci, Portland, OR 97239 USA
Margaret Ferris - Univ Illinois, Urbana, IL 61801 USA
Christopher N. Balakrishnan - Univ Illinois, Urbana, IL 61801 USA
Saurabh Sinha - Univ Illinois, Urbana, IL 61801 USA
Charles Blatti - Univ Illinois, Urbana, IL 61801 USA
Sarah E. London - Univ Illinois, Urbana, IL 61801 USA
Yun Li - Univ Illinois, Urbana, IL 61801 USA
Ya-Chi Lin - Univ Illinois, Urbana, IL 61801 USA
Julia George - Univ Illinois, Urbana, IL 61801 USA
Jonathan Sweedler - University of Illinois Urbana-Champaign
Bruce Southey - Univ Illinois, Urbana, IL 61801 USA
Preethi Gunaratne - Univ Houston, Dept Biol & Biochem, Houston, TX 77204 USA
Michael Watson - Inst Anim Hlth, Dept Bioinformat, Compton RG20 7NN, Berks, England
Kiwoong Nam - Uppsala Univ, Inst Evolut & Genet Syst, S-75236 Uppsala, Sweden
Niclas Backstroem - Uppsala Univ, Inst Evolut & Genet Syst, S-75236 Uppsala, Sweden
Linnea Smeds - Uppsala University
Benoit Nabholz - Uppsala Univ, Inst Evolut & Genet Syst, S-75236 Uppsala, Sweden
Yuichiro Itoh - Univ Calif Los Angeles, Los Angeles, CA 90056 USA
Osceola Whitney - Duke Univ, Med Ctr, Dept Neurobiol, Howard Hughes Med Inst, Durham, NC 27710 USA
Andreas R. Pfenning - Duke Univ, Med Ctr, Dept Neurobiol, Howard Hughes Med Inst, Durham, NC 27710 USA
Jason Howard - Duke University
Martin Voelker - Inst Anim Hlth, Dept Bioinformat, Compton RG20 7NN, Berks, England
Bejamin M. Skinner - Univ Kent, Dept Biosci, Canterbury CT2 7NJ, Kent, England
Darren K. Griffin - Univ Kent, Dept Biosci, Canterbury CT2 7NJ, Kent, England
Liang Ye - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
William M. McLaren - European Bioinformatics Institute
Paul Flicek - Oregon Hlth & Sci Univ, Dept Behav Neurosci, Portland, OR 97239 USA
Victor Quesada - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Gloria Velasco - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Carlos Lopez-Otin - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Xose S. Puente - Univ Oviedo, Dept Bioquim & Biol Mol, Inst Univ Oncol, E-33006 Oviedo, Spain
Tsviya Olender - Weizmann Inst Sci, Dept Mol Genet, Crown Human Genome Ctr, IL-76100 Rehovot, Israel
Doron Lancet - Weizmann Inst Sci, Dept Mol Genet, Crown Human Genome Ctr, IL-76100 Rehovot, Israel
Arian F. A. Smit - Inst Syst Biol, Seattle, WA 98103 USA
Robert Hubley - Inst Syst Biol, Seattle, WA 98103 USA
Miriam K. Konkel - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Jerilyn A. Walker - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Mark A. Batzer - Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
Wanjun Gu - Univ Colorado, Hlth Sci Ctr, Dept Biochem & Mol Genet, Aurora, CO 80045 USA
David D. Pollock - Univ Colorado, Hlth Sci Ctr, Dept Biochem & Mol Genet, Aurora, CO 80045 USA
Lin Chen - Univ Washington, Seattle, WA 98195 USA
Ze Cheng - Univ Washington, Seattle, WA 98195 USA
Evan E. Eichler - University of Washington
Jessica Stapley - Univ Washington, Seattle, WA 98195 USA
Jon Slate - University of Sheffield
Robert Ekblom - Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England
Tim Birkhead - Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England
Terry Burke - Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England
David Burt - Univ Edinburgh, Roslin Inst, Edinburgh EH25 9OS, Midlothian, Scotland
Constance Scharff - Free Univ Berlin, Inst Biol, D-14195 Berlin, Germany
Iris Adam - Free Univ Berlin, Inst Biol, D-14195 Berlin, Germany
Hugues Richard - Max Planck Inst Mol Genet, Dept Vertebrate Genom, D-14195 Berlin, Germany
Marc Sultan - Max Planck Inst Mol Genet, Dept Vertebrate Genom, D-14195 Berlin, Germany
Alexey Soldatov - Max Planck Inst Mol Genet, Dept Vertebrate Genom, D-14195 Berlin, Germany
Hans Lehrach - Max Planck Inst Mol Genet, Dept Vertebrate Genom, D-14195 Berlin, Germany
Scott V. Edwards - Harvard University
Shiaw-Pyng Yang - Monsanto Co, St Louis, MO 63167 USA
XiaoChing Li - Louisiana State Univ, Hlth Sci Ctr, Ctr Neurosci, New Orleans, LA 70112 USA
Tina Graves - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Lucinda Fulton - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Joanne Nelson - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Asif Chinwalla - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Shunfeng Hou - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Elaine R. Mardis - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Richard K. Wilson - Washington Univ, Genome Ctr, Sch Med, St Louis, MO 63108 USA
Détails de publication: Nature (London), Vol.464(7289), pp.757-762
Éditeur: Springer Nature
Nombre de pages: 6
Note de subvention: National Human Genome Research Institute (NHGRI); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) RO1 NS045264; RO1 NS051820; R01 DC007218; RO1 GM59290 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA GRANTS:15400207; BB/E017509/1; BBS/E/I/00001425; GRANTS:15388109; GRANTS:15345674; BB/E010652/1; GRANTS:15335652; BB/D013704/1; BB/D013704/2; BB/F007590/1; GRANTS:15394035; GRANTS:15397361 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MC_U137761446; GRANTS:15368937 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) GRANTS:14924129; BB/D013704/2; GRANTS:14891869; BBS/E/I/00001425; GRANTS:14923147; BB/E017509/1; GRANTS:14920860; BB/E010652/1; BB/F007590/1; GRANTS:14927653; GRANTS:14941686; BB/D013704/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) BBE0175091 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Swedish Research Council Knut and Alice Wallenberg Foundation; Knut & Alice Wallenberg Foundation GRANTS:14899939; MC_U137761446 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC)
Identifiants: 99146376609311
Unité académique: Institut des Sciences de l'Evolution - Montpellier - ISEM
Langue: English
Type de ressource: Journal article