The genome of a songbird

Wesley C. Warren; David F. Clayton; Hans Ellegren; Arthur P. Arnold; Ladeana W. Hillier; Axel Künstner; 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 Backström; Linnea Smeds; Benoit Nabholz; Yuichiro Itoh; Osceola Whitney; Andreas R. Pfenning; Jason Howard; Martin Völker; 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

The genome of a songbird

Wesley C. Warren, David F. Clayton, Hans Ellegren, Arthur P. Arnold, Ladeana W. Hillier, Axel Künstner, 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. BalakrishnanSaurabh Sinha, Charles Blatti, Sarah E. London, Yun Li, Ya-Chi Lin, Julia George, Jonathan Sweedler, Bruce Southey, Preethi Gunaratne, Michael Watson, Kiwoong Nam, Niclas Backström, Linnea Smeds, Benoit Nabholz, Yuichiro Itoh, Osceola Whitney, Andreas R. Pfenning, Jason Howard, Martin Völker, 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

Applied Medicine

Research output: Contribution to journal › Article › peer-review

635 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	757-762
Number of pages	6
Journal	Nature
Volume	464
Issue number	7289
DOIs	https://doi.org/10.1038/nature08819
Publication status	Published - 1 Apr 2010

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Warren, W. C., Clayton, D. F., Ellegren, H., Arnold, A. P., Hillier, L. W., Künstner, A., Searle, S., White, S., Vilella, A. J., Fairley, S., Heger, A., Kong, L., Ponting, C. P., Jarvis, E. D., Mello, C. V., Minx, P., Lovell, P., Velho, T. A. F., Ferris, M., ... Wilson, R. K. (2010). The genome of a songbird. Nature, 464(7289), 757-762. https://doi.org/10.1038/nature08819

Warren, WC, Clayton, DF, Ellegren, H, Arnold, AP, Hillier, LW, Künstner, A, Searle, S, White, S, Vilella, AJ, Fairley, S, Heger, A, Kong, L, Ponting, CP, Jarvis, ED, Mello, CV, Minx, P, Lovell, P, Velho, TAF, Ferris, M, Balakrishnan, CN, Sinha, S, Blatti, C, London, SE, Li, Y, Lin, Y-C, George, J, Sweedler, J, Southey, B, Gunaratne, P, Watson, M, Nam, K, Backström, N, Smeds, L, Nabholz, B, Itoh, Y, Whitney, O, Pfenning, AR, Howard, J, Völker, M, Skinner, BM, Griffin, DK, Ye, L, McLaren, WM, Flicek, P, Quesada, V, Velasco, G, Lopez-Otin, C, Puente, XS, Olender, T, Lancet, D, Smit, AFA, Hubley, R, Konkel, MK, Walker, JA, Batzer, MA, Gu, W, Pollock, DD, Chen, L, Cheng, Z, Eichler, EE, Stapley, J, Slate, J, Ekblom, R, Birkhead, T, Burke, T, Burt, D, Scharff, C, Adam, I, Richard, H, Sultan, M, Soldatov, A, Lehrach, H, Edwards, SV, Yang, S-P, Li, X, Graves, T, Fulton, L, Nelson, J, Chinwalla, A, Hou, S, Mardis, ER & Wilson, RK 2010, 'The genome of a songbird', Nature, vol. 464, no. 7289, pp. 757-762. https://doi.org/10.1038/nature08819

@article{0dd543a6273f42c9b6e2c1e3594e71f3,

title = "The genome of a songbird",

abstract = "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.",

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

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T1 - The genome of a songbird

AU - Warren, Wesley C.

AU - Clayton, David F.

AU - Ellegren, Hans

AU - Arnold, Arthur P.

AU - Hillier, Ladeana W.

AU - Künstner, Axel

AU - Searle, Steve

AU - White, Simon

AU - Vilella, Albert J.

AU - Fairley, Susan

AU - Heger, Andreas

AU - Kong, Lesheng

AU - Ponting, Chris P.

AU - Jarvis, Erich D.

AU - Mello, Claudio V.

AU - Minx, Pat

AU - Lovell, Peter

AU - Velho, Tarciso A. F.

AU - Ferris, Margaret

AU - Balakrishnan, Christopher N.

AU - Sinha, Saurabh

AU - Blatti, Charles

AU - London, Sarah E.

AU - Li, Yun

AU - Lin, Ya-Chi

AU - George, Julia

AU - Sweedler, Jonathan

AU - Southey, Bruce

AU - Gunaratne, Preethi

AU - Watson, Michael

AU - Nam, Kiwoong

AU - Backström, Niclas

AU - Smeds, Linnea

AU - Nabholz, Benoit

AU - Itoh, Yuichiro

AU - Whitney, Osceola

AU - Pfenning, Andreas R.

AU - Howard, Jason

AU - Völker, Martin

AU - Skinner, Bejamin M

AU - Griffin, Darren K.

AU - Ye, Liang

AU - McLaren, William M.

AU - Flicek, Paul

AU - Quesada, Victor

AU - Velasco, Gloria

AU - Lopez-Otin, Carlos

AU - Puente, Xose S.

AU - Olender, Tsviya

AU - Lancet, Doron

AU - Smit, Arian F. A.

AU - Hubley, Robert

AU - Konkel, Miriam K.

AU - Walker, Jerilyn A.

AU - Batzer, Mark A.

AU - Gu, Wanjun

AU - Pollock, David D.

AU - Chen, Lin

AU - Cheng, Ze

AU - Eichler, Evan E.

AU - Stapley, Jessica

AU - Slate, Jon

AU - Ekblom, Robert

AU - Birkhead, Tim

AU - Burke, Terry

AU - Burt, David

AU - Scharff, Constance

AU - Adam, Iris

AU - Richard, Hugues

AU - Sultan, Marc

AU - Soldatov, Alexey

AU - Lehrach, Hans

AU - Edwards, Scott V.

AU - Yang, Shiaw-Pyng

AU - Li, Xiaoching

AU - Graves, Tina

AU - Fulton, Lucinda

AU - Nelson, Joanne

AU - Chinwalla, Asif

AU - Hou, Shunfeng

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

PY - 2010/4/1

Y1 - 2010/4/1

N2 - 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.

AB - 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.

U2 - 10.1038/nature08819

DO - 10.1038/nature08819

M3 - Article

C2 - 20360741

VL - 464

SP - 757

EP - 762

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7289

ER -

The genome of a songbird

Abstract

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