The genome of a songbird
Wesley C. Warren
(1)
,
David F. Clayton
(2)
,
Hans Ellegren
(3)
,
Arthur P. Arnold
(4)
,
Ladeana W. Hillier
(1)
,
Axel Künstner
(3)
,
Steve Searle
(5)
,
Simon White
(5)
,
Albert J. Vilella
(6)
,
Susan Fairley
(5)
,
Andreas Heger
(7)
,
Lesheng Kong
(7)
,
Chris P. Ponting
(7)
,
Erich D. Jarvis
(8)
,
Claudio V. Mello
(9)
,
Pat Minx
(1)
,
Peter Lovell
(9)
,
Tarciso A. F. Velho
(9)
,
Margaret Ferris
(10)
,
Christopher N. Balakrishnan
(10)
,
Saurabh Sinha
(10)
,
Charles Blatti
(10)
,
Sarah E. London
(10)
,
Yun Li
(10)
,
Ya-Chi Lin
(2)
,
Julia George
(10)
,
Jonathan Sweedler
(10)
,
Bruce Southey
(10)
,
Preethi Gunaratne
(11)
,
Michael Watson
(12)
,
Ki Woong Nam
(3)
,
Niclas Backström
(3)
,
Linnea Smeds
(3)
,
Benoit Nabholz
(3)
,
Yuichiro Itoh
(4)
,
Osceola Whitney
(8)
,
Andreas R. Pfenning
(8)
,
Jason Howard
(8)
,
Martin Völker
(12)
,
Bejamin M. Skinner
(13)
,
Darren K. Griffin
(13)
,
Liang Ye
(1)
,
William M. Mclaren
(6)
,
Paul Flicek
(6)
,
Victor Quesada
(14)
,
Gloria Velasco
(14)
,
Carlos López-Otín
(14)
,
Xose S. Puente
(14)
,
Tsviya Olender
(15)
,
Doron Lancet
(15)
,
Arian F. A. Smit
(16)
,
Robert Hubley
(16)
,
Miriam K. Konkel
(17)
,
Jerilyn A. Walker
(17)
,
Mark A. Batzer
(17)
,
Wanjun Gu
(18)
,
David D. Pollock
(18)
,
Lin Chen
(19)
,
Ze Cheng
(19)
,
Evan E. Eichler
(19)
,
Jessica Stapley
(19)
,
Jon Slate
(20)
,
Robert Ekblom
(20)
,
Tim Birkhead
(20)
,
Terry Burke
(20)
,
David Burt
(21)
,
Constance Scharff
(22)
,
Iris Adam
(22)
,
Hugues Richard
(23)
,
Marc Sultan
(23)
,
Alexey Soldatov
(23)
,
Hans Lehrach
(23)
,
Scott V Edwards
(24)
,
Shiaw-Pyng Yang
(25)
,
Xiaoching Li
(26)
,
Tina Graves
(1)
,
Lucinda Fulton
(1)
,
Joanne Nelson
(1)
,
Asif Chinwalla
(1)
,
Shunfeng Hou
(1)
,
Elaine R. Mardis
(1)
,
Richard K. Wilson
(1)
1
The Genome Center
2 University of Illinois System
3 Uppsala University
4 UCLA - University of California [Los Angeles]
5 The Wellcome Trust Sanger Institute [Cambridge]
6 European Molecular Biology Laboratory European Bioinformatics Institute
7 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics
8 Duke University Medical Center
9 Oregon Health & Science University
10 UIUC - University of Illinois at Urbana-Champaign [Urbana]
11 Department of Biology & Biochemistry
12 Institute for Animal Health
13 University of Kent
14 Universidad de Oviedo [Oviedo]
15 Weizmann Institute of Science [Rehovot, Israël]
16 ISB - Institute for Systems Biology [Seattle]
17 Department of Biological Sciences
18 University of Colorado
19 Genome sciences
20 Department of Animal & Plant Sciences
21 The Roslin Institute and Royal (Dick) School of Veterinary Studies
22 FU - Free University of Berlin
23 Department of Vertebrate Genomics
24 Department of Organismic and Evolutionary Biology
25 Monsanto Company
26 LSU - Louisiana State University
2 University of Illinois System
3 Uppsala University
4 UCLA - University of California [Los Angeles]
5 The Wellcome Trust Sanger Institute [Cambridge]
6 European Molecular Biology Laboratory European Bioinformatics Institute
7 MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics
8 Duke University Medical Center
9 Oregon Health & Science University
10 UIUC - University of Illinois at Urbana-Champaign [Urbana]
11 Department of Biology & Biochemistry
12 Institute for Animal Health
13 University of Kent
14 Universidad de Oviedo [Oviedo]
15 Weizmann Institute of Science [Rehovot, Israël]
16 ISB - Institute for Systems Biology [Seattle]
17 Department of Biological Sciences
18 University of Colorado
19 Genome sciences
20 Department of Animal & Plant Sciences
21 The Roslin Institute and Royal (Dick) School of Veterinary Studies
22 FU - Free University of Berlin
23 Department of Vertebrate Genomics
24 Department of Organismic and Evolutionary Biology
25 Monsanto Company
26 LSU - Louisiana State University
Ki Woong Nam
- Fonction : Auteur
- PersonId : 1252956
- IdHAL : kiwoong-nam
- ORCID : 0000-0003-3194-8673
Benoit Nabholz
- Fonction : Auteur
- PersonId : 737780
- IdHAL : benoit-nabholz
- ORCID : 0000-0003-0447-1451
- IdRef : 129854174
Paul Flicek
- Fonction : Auteur
- PersonId : 769433
- ORCID : 0000-0002-3897-7955
Hugues Richard
- Fonction : Auteur
- PersonId : 14119
- IdHAL : hugues-richard
- IdRef : 061687391
Résumé
The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. 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-the only bird with a sequenced genome until now. 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. 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.