The genome of a songbird

  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 M 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 Xose 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},
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… 

The neurobiology of Zebra Finch song: insights from gene expression studies

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.

Songbird genome provides clues about speech

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

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
    Cold Spring Harbor protocols
  • 2014
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

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.

High-coverage sequencing and annotated assemblies of the budgerigar genome

Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble.

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

Brain transcriptomes for three emberizid model systems are presented and tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile is found.

The zebra finch neuropeptidome: prediction, detection and expression

Interestingly, most mammalian prohormones have counterparts in the zebra finch, demonstrating that this songbird uses similar biochemical pathways for neurotransmission and hormonal regulation.

The Zebra Finch genome and avian genomics in the wild

The genomic resources available for the Zebra Finch, including the genome sequence itself, are discussed, and some of the ways in which they will facilitate the study of avian diversity are highlighted.

The genome of the green anole lizard and a comparative analysis with birds and mammals

Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins, and an anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.



The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution

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

A Linkage Map of the Zebra Finch Taeniopygia guttata Provides New Insights Into Avian Genome Evolution

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.

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

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

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

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

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

Discrete molecular states in the brain accompany changing responses to a vocal signal

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.