Du är här

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

Författare:
  • Kirstin Replogle
  • Arthur P Arnold
  • Gregory F Ball
  • Mark Band
  • Staffan Bensch
  • Eliot A Brenowitz
  • Shu Dong
  • Jenny Drnevich
  • Margaret Ferris
  • Julia M. George
  • George Gong
  • Dennis Hasselquist
  • Alvaro G Hernandez
  • Ryan Kim
  • Harris A Lewin
  • Lei Liu
  • Peter V Lovell
  • Claudio V Mello
  • Sara Naurin
  • Sandra Rodriguez-Zas
  • Jyothi Thimmapuram
  • Juli Wade
  • David F Clayton
Publiceringsår: 2008
Språk: Engelska
Publikation/Tidskrift/Serie: BMC Genomics
Volym: 9
Nummer: 131
Dokumenttyp: Artikel
Förlag: BioMed Central Ltd.

Sammanfattning

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 similar to 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.

Disputation

Nyckelord

  • Biology and Life Sciences

Övriga

Published
Yes
  • Molecular Ecology and Evolution Lab
  • ISSN: 1471-2164

Box 117, 221 00 LUND
Telefon 046-222 00 00 (växel)
Telefax 046-222 47 20
lu [at] lu [dot] se

 

Fakturaadress: Box 188, 221 00 LUND
Organisationsnummer: 202100-3211
Om webbplatsen