High-Speed Developments in Avian Genomics

  title={High-Speed Developments in Avian Genomics},
  author={Camille Bonneaud and Joan Burnside and Scott V. Edwards},
ABSTRACT Until recently, definitions of avian genome structure and function were based solely on our knowledge of the chicken genome. The expansion of genomic studies to include nonmodel avian species allows us not only to refine those definitions but also to begin collecting the necessary resources to initiate a truly ecological genomics of birds. In this article we review new genomic technologies that will speed up the investigation of avian genome function. The streamlined nature of avian… 

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome.

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

The results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles.

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The status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and the present and future vision of the landscape of Genome 10K are provided.

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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.

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The avian genome uncovered.

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Current approaches and data characteristics of recent higher-level bird studies are summarized and a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds are suggested.

Functional genomics of the chicken--a model organism.

Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird.

Molecular evolutionary genomics of birds

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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.

Chicken genome: current status and future opportunities.

The chicken genome sequence is important because it fills a gap in knowledge and understanding of the evolution and conservation of genes, regulatory sequences, genomes, and karyotypes, and it is the first livestock species to be sequenced and so leads the way for others.

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BAC libraries and comparative genomics of aquatic chordate species.

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  • Biology
    Comparative biochemistry and physiology. Toxicology & pharmacology : CBP
  • 2004

Strong regional biases in nucleotide substitution in the chicken genome.

Analysis of variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing the present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum likelihood model suggests that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.