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Open Access Highly Accessed Research article

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

Kirstin Replogle19, Arthur P Arnold2, Gregory F Ball3, Mark Band8, Staffan Bensch11, Eliot A Brenowitz4, Shu Dong1, Jenny Drnevich8, Margaret Ferris12, Julia M George5, George Gong8, Dennis Hasselquist11, Alvaro G Hernandez8, Ryan Kim8, Harris A Lewin109, Lei Liu8, Peter V Lovell6, Claudio V Mello6, Sara Naurin11, Sandra Rodriguez-Zas10, Jyothi Thimmapuram8, Juli Wade7 and David F Clayton1129*

Author Affiliations

1 Cell & Developmental Biology, Univ. of Illinois, Urbana, IL, USA

2 Physiological Sci., UCLA, Los Angeles, CA, USA

3 Psychological & Brain Sci., Johns Hopkins Univ., Baltimore, MD, USA

4 Psychology, Biology, and Bloedel Hearing Research Center, Univ. of Washington, Seattle, WA, USA

5 Mol. & Integrative Physiology, Univ. of Illinois, Urbana, IL, USA

6 Neurological Sci. Inst., Oregon Hlth. Sci. Univ., Beaverton, OR, USA

7 Psychology, Zoology & Neuroscience, Michigan State Univ., East Lansing, MI, USA

8 W.M. Keck Center for Comparative & Functional Genomics, Univ. of Illinois, Urbana, IL, USA

9 Institute for Genomic Biology, Univ. of Illinois, Urbana, IL, USA

10 Animal Sciences, Univ. of Illinois, Urbana, IL, USA

11 Animal Ecology, Lund University, S-223 62 Lund, Sweden

12 Neuroscience Program, Univ. of Illinois, Urbana, IL, USA

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BMC Genomics 2008, 9:131  doi:10.1186/1471-2164-9-131

Published: 18 March 2008

Abstract

Background

Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.

Results

We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500–15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.

Conclusion

Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.