The genome of a songbird.
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.
Warren
Wesley C
WC
The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@watson.wustl.edu
Clayton
David F
DF
Ellegren
Hans
H
Arnold
Arthur P
AP
Hillier
Ladeana W
LW
Künstner
Axel
A
Searle
Steve
S
White
Simon
S
Vilella
Albert J
AJ
Fairley
Susan
S
Heger
Andreas
A
Kong
Lesheng
L
Ponting
Chris P
CP
Jarvis
Erich D
ED
Mello
Claudio V
CV
Minx
Pat
P
Lovell
Peter
P
Velho
Tarciso A F
TA
Ferris
Margaret
M
Balakrishnan
Christopher N
CN
Sinha
Saurabh
S
Blatti
Charles
C
London
Sarah E
SE
Li
Yun
Y
Lin
Ya-Chi
YC
George
Julia
J
Sweedler
Jonathan
J
Southey
Bruce
B
Gunaratne
Preethi
P
Watson
Michael
M
Nam
Kiwoong
K
Backström
Niclas
N
Smeds
Linnea
L
Nabholz
Benoit
B
Itoh
Yuichiro
Y
Whitney
Osceola
O
Pfenning
Andreas R
AR
Howard
Jason
J
Völker
Martin
M
Skinner
Bejamin M
BM
Griffin
Darren K
DK
Ye
Liang
L
McLaren
William M
WM
Flicek
Paul
P
Quesada
Victor
V
Velasco
Gloria
G
Lopez-Otin
Carlos
C
Puente
Xose S
XS
Olender
Tsviya
T
Lancet
Doron
D
Smit
Arian F A
AF
Hubley
Robert
R
Konkel
Miriam K
MK
Walker
Jerilyn A
JA
Batzer
Mark A
MA
Gu
Wanjun
W
Pollock
David D
DD
Chen
Lin
L
Cheng
Ze
Z
Eichler
Evan E
EE
Stapley
Jessica
J
Slate
Jon
J
Ekblom
Robert
R
Birkhead
Tim
T
Burke
Terry
T
Burt
David
D
Scharff
Constance
C
Adam
Iris
I
Richard
Hugues
H
Sultan
Marc
M
Soldatov
Alexey
A
Lehrach
Hans
H
Edwards
Scott V
SV
Yang
Shiaw-Pyng
SP
Li
Xiaoching
X
Graves
Tina
T
Fulton
Lucinda
L
Nelson
Joanne
J
Chinwalla
Asif
A
Hou
Shunfeng
S
Mardis
Elaine R
ER
Wilson
Richard K
RK
D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D001307:Auditory Perception / Q000235:genetics; D001921:Brain / Q000502:physiology; D002645:Chickens / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D046369:Finches / Q000235:genetics* / Q000502:physiology; D020440:Gene Duplication; D053263:Gene Regulatory Networks / Q000235:genetics; D016678:Genome / Q000235:genetics*; D008297:Male; D035683:MicroRNAs / Q000235:genetics; D023421:Models, Animal; D005810:Multigene Family / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D012730:Sex Chromosomes / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics; D014828:Vocalization, Animal / Q000502:physiology
D020413:3' Untranslated Regions; D035683:MicroRNAs; D018626:Retroelements