Free Standard AU & NZ Shipping For All Book Orders Over $80!
Register      Login
Emu Emu Society
Journal of BirdLife Australia
Shopping Cart: ( empty )
You are here: Home > Journals > MU > MU09087
REVIEW
Contents Vol 110(3)

The Zebra Finch genome and avian genomics in the wild

Christopher N. Balakrishnan A C , Scott V. Edwards B and David F. Clayton A
+ Author Affiliations
- Author Affiliations

A Department of Cell and Developmental Biology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61820, USA.

B Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

C Corresponding author. Email: cbala@igb.uiuc.edu

Emu 110(3) 233-241 https://doi.org/10.1071/MU09087
Submitted: 3 September 2009  Accepted: 12 January 2010   Published: 18 August 2010

Abstract

The Zebra Finch (Taeniopygia guttata) is the first species of passerine bird with a complete genome sequence, making it an exciting time for avian evolutionary biology. Native to Australia and the Lesser Sunda Islands, this species has long played an important role in the study of ecology, behaviour and neuroscience. With the sequencing of its genome, the Zebra Finch now also represents an important model system for evolutionary and population genomics. The production of a genome sequence for the Zebra Finch will have far-reaching impacts on the study of avian biology. Here we discuss the genomic resources available for the Zebra Finch, including the genome sequence itself, and some of the ways in which they will facilitate the study of avian diversity. We also highlight recent examples from the literature that have already begun to leverage Zebra Finch genomic tools towards the study of birds in nature.


References

Åkesson, M. , Hansson, B. , Hasselquist, D. , and Bensch, S. (2007). Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals. Molecular Ecology 16, 2189–2202.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Arnold A. P. , and Clayton D. F. (2002). Proposal for construction of a BAC library of the genome of the Zebra Finch (Taeniopygia guttata). Available at http://songbirdgenome.org/pdfs/NHGRI-ZF-BAC.pdf [Verified 29 July 2010].

Avise J. C. (1994). ‘Molecular Markers, Natural History and Evolution.’ (Chapman and Hall: New York.)

Backström, N. , Karaiskou, N. , Leder, E. H. , Gustafsson, L. , Primmer, C. R. , Qvarnström, A. , and Ellegren, H. (2008a). A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene-order conservation during 100 million years of avian evolution. Genetics 179, 1479–1495.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Balakrishnan C. N. , Lee J. Y. , and Edwards S. V. (2010a). Phylogeography and phylogenetics in the Nuclear Age. In ‘In Search of the Causes of Evolution: From Field Observations to Mechanisms’. (Eds P. R. Grant and R. Grant.) (Princeton University Press: Princeton, NJ.).

Balakrishnan, C. N. , Ekblom, R. , Volker, M. , Westerdahl, H. , Godinez, R. , Burt, D. W. , Graves, T. , Griffin, D. K. , Warren, W. C. , and Edwards, S. V. (2010b). Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biology 8, 29.
| Crossref | GoogleScholarGoogle Scholar | PubMed | Clayton D. , Arnold A. P. , Warren W. C. , and Dodgson J. (2005 a). Proposal for construction of a physical map of the genome of the Zebra Finch (Taeniopygia guttata). Available at http://songbirdgenome.org/pdfs/NHGRI-ZF-map.pdf [Verified 22 July 2010].

Clayton D. F. , Arnold A. P. , Warren W. , Jarvis E. , Mello C. , Burt D. W. , and Ellegren H. (2005 b). Proposal to sequence the genome of the Zebra Finch (Taeniopygia guttata). Available at http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/ZebraFinchSeq2.pdf [Verified 22 July 2010].

Couzin, J. (2002). NSF’s ark draws alligators, algae and wasps. Science 297, 1638–1639.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | Goodwin D. (1982). ‘Estrildid Finches of the World.’ (Cornell University Press: Ithaca, NY.)

Hansson, B. , Åkesson, M. , Slate, J. , and Pemberton, J. M. (2005). Linkage mapping reveals sex-dimorphic map distances in a passerine bird. Proceedings of the Royal Society of London. Series B. Biological Sciences 272, 2289–2298.
| Crossref | GoogleScholarGoogle Scholar | CAS | Shedlock A. M. , Janes D. E. , and Edwards S. V. (2008). Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. In ‘Phylogenomics’. (Ed. W. Murphy.) pp. 97–117. (Humana Press: Totowa, NJ.)

Shiina, T. , Shimizu, S. , Hosomichi, K. , Kohara, S. , Watanabe, S. , Hanzawa, K. , Beck, S. , Kulski, J. K. , and Inoko, H. (2004). Comparative genomic analysis of two avian (quail and chicken) MHC regions. Journal of Immunology 172, 6751–6763.
|  CAS | Wakeley J. (2008). ‘Coalescent Theory: An Introduction.’ (Roberts & Company: Greenwood Village, CO, USA.)

Wakeley, J. , Nielsen, R. , Liu-Cordero, S. N. , and Ardlie, K. (2001). The discovery of single-nucleotide polymorphisms – and inferences about human demographic history. American Journal of Human Genetics 69, 1332–1347.
| Crossref | GoogleScholarGoogle Scholar | CAS | PubMed | Zann R. A. (1996). ‘The Zebra Finch: A Synthesis of Field and Laboratory Studies.’ (Oxford University Press: New York.)