The genome of a songbird

@article{Warren2010TheGO,
  title={The genome of a songbird},
  author={Wesley C. Warren and David F. Clayton and Hans Ellegren and Arthur P. Arnold and LaDeana W. Hillier and Axel K{\"u}nstner and Stephen M. J. Searle and Simon White and Albert J. Vilella and Susan Fairley and Andreas Heger and Lesheng Kong and Chris Paul Ponting and Erich D. Jarvis and Claudio V. Mello and Patrick Minx and Peter V. Lovell and Tarciso A. F. Velho and Margaret Ferris and Christopher N. Balakrishnan and Saurabh Sinha and Charles A Blatti and Sarah E. London and Yun Li and Ya-Chi Lin and Julia M. George and Jonathan V. Sweedler and Bruce R. Southey and Preethi H. Gunaratne and Michael Watson and Kiwoong Nam and Niclas Backstr{\"o}m and Linn{\'e}a Smeds and Benoit Nabholz and Yuichiro Itoh and Osceola Whitney and Andreas R. Pfenning and Jason T. Howard and Martin V{\"o}lker and Bejamin M. Skinner and Darren K. Griffin and Liang Ye and William M. McLaren and Paul Flicek and V{\'i}ctor Quesada and Gloria Velasco and Carlos L{\'o}pez-Ot{\'i}n and Xos{\'e} S. Puente and Tsviya Olender and Doron Lancet and Arian F. A. Smit and Robert M. Hubley and Miriam K. Konkel and Jerilyn A. Walker and Mark A. Batzer and Wanjun Gu and David D. Pollock and Lin Chen and Ze Cheng and Evan E. Eichler and Jessica Stapley and Jon Slate and Robert Ekblom and Tim R. Birkhead and Terry A Burke and David W. Burt and Constance Scharff and Iris Adam and Hugues Richard and Marc Sultan and A. F. Soldatov and Hans Lehrach and Scott V. Edwards and Shiaw-Pyng Yang and XiaoChing Li and Tina Graves and Lucinda A. Fulton and Joanne O. Nelson and Asif T. Chinwalla and Shunfeng Hou and Elaine R. Mardis and Richard K. Wilson},
  journal={Nature},
  year={2010},
  volume={464},
  pages={757-762}
}
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… 
Comparative genomics reveals molecular features unique to the songbird lineage
TLDR
This study reveals novel genes unique to songbirds, including some that may subserve their unique vocal control system, substantially improves the quality of Zebra finch genome annotations, and contributes to a better understanding of how genomic features may have evolved in conjunction with the emergence of the songbird lineage.
The neurobiology of Zebra Finch song: insights from gene expression studies
TLDR
The major components of the song system are introduced and evidence for how each might contribute to these three aspects of song is described, including the structural organisation and functional activities of the neural system underlying vocal communication.
Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary
Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird
Molecular evolution of genes in avian genomes
TLDR
There was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution, and these findings set the stage for studies of functional genetics of avian genes.
Songbird genome provides clues about speech
TLDR
Wesley Warren of the University of Washington in St. Louis, MO, and colleagues sequenced the genome of a male zebra finch and then compared this genome with that of a chicken, the only other bird whose genome has been sequenced to date.
Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome
TLDR
Genome-wide ω was identical in zebra finch and violet-eared waxbill lineages, suggesting a similar demographic history with efficient purifying natural selection, and further comparisons of these and other estrildid finches may provide insights into the evolutionary neurogenomics of social behaviour.
The zebra finch, Taeniopygia guttata: an avian model for investigating the neurobiological basis of vocal learning.
  • C. Mello
  • Biology, Medicine
    Cold Spring Harbor protocols
  • 2014
TLDR
Zebra finches have emerged as a choice model organism for investigating the neurobiological basis of vocal learning and a number of tools and methodologies have been developed to characterize the bioacoustics properties of their song, analyze the degree of accurate copying during vocal learning, map the brain circuits that control singing and song learning, and investigate the physiology of these circuits.
Gene manipulation to test links between genome, brain and behavior in developing songbirds: a test case
TLDR
This Review uses one area of zebra finch song learning to demonstrate how genome editing can advance causal investigations into known genome–brain–behavior relationships.
Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
TLDR
A genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community and reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.
Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning
TLDR
A draft Bengalese finch genome and gene annotation is provided to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning, enabling novel mechanistic investigations into the role of variability in learned behavior.
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References

SHOWING 1-10 OF 44 REFERENCES
The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
TLDR
A core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts are developed and a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds are planned.
Integrating Genomes, Brain and Behavior in the Study of Songbirds
TLDR
The distinctive organization of the songbird brain will facilitate analysis of genomic links to brain and behavior, and access to the zebra finch genome sequence will prompt new questions and provide the ability to answer them.
A Linkage Map of the Zebra Finch Taeniopygia guttata Provides New Insights Into Avian Genome Evolution
TLDR
A whole-genome linkage map for the zebra finch using a 354-bird pedigree is constructed and there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes.
Song presentation induces gene expression in the songbird forebrain.
TLDR
Results suggest a role for genomic responses in neural processes linked to song pattern recognition, discrimination, or the formation of auditory associations in songbird brain response to birdsong.
Birdsong “Transcriptomics”: Neurochemical Specializations of the Oscine Song System
TLDR
The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood.
Transgenic songbirds offer an opportunity to develop a genetic model for vocal learning
TLDR
An HIV-based lentivirus was injected into the very early embryo to target the primordial germline cells that later give rise to sperm and eggs and produced germline transgenic hatchlings that expressed the GFP protein (F1).
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
TLDR
A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes
TLDR
This work constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of zebra finches in 57 developmental and behavioral conditions in an attempt to clone as much of the brain transcriptome as possible.
Habituation in songbirds
TLDR
There are strong correlations between habituation measurements made at these different levels, but some dissociations have also been observed, implying that molecular, electrophysiological and behavioral habituations are not equivalent manifestations of a single core process.
Discrete molecular states in the brain accompany changing responses to a vocal signal
TLDR
It is shown that novel song exposure induces rapid changes in thousands of RNAs, with even more RNAs decreasing than increasing, and a natural experience, in this case hearing the sound of birdsong, can lead to major shifts in energetics and macromolecular metabolism in higher centers in the brain.
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