title: The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution.
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 approximately 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.
  
  
  CONCLUSIONS
  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.
authors: Cell & Developmental Biology, Univ, of Illinois, Urbana, IL, USA. replogle@igb.uiuc.edu
authors: Kirstin
authors: K
authors: Replogle
authors: Arthur P
authors: AP
authors: Arnold
authors: Gregory F
authors: GF
authors: Ball
authors: Mark
authors: M
authors: Band
authors: Staffan
authors: S
authors: Bensch
authors: Eliot A
authors: EA
authors: Brenowitz
authors: Shu
authors: S
authors: Dong
authors: Jenny
authors: J
authors: Drnevich
authors: Margaret
authors: M
authors: Ferris
authors: Julia M
authors: JM
authors: George
authors: George
authors: G
authors: Gong
authors: Dennis
authors: D
authors: Hasselquist
authors: Alvaro G
authors: AG
authors: Hernandez
authors: Ryan
authors: R
authors: Kim
authors: Harris A
authors: HA
authors: Lewin
authors: Lei
authors: L
authors: Liu
authors: Peter V
authors: PV
authors: Lovell
authors: Claudio V
authors: CV
authors: Mello
authors: Sara
authors: S
authors: Naurin
authors: Sandra
authors: S
authors: Rodriguez-Zas
authors: Jyothi
authors: J
authors: Thimmapuram
authors: Juli
authors: J
authors: Wade
authors: David F
authors: DF
authors: Clayton
mesh_terms: D000161:Acoustic Stimulation; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D017874:Immediate-Early Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D020308:Songbirds / Q000235:genetics* / Q000502:physiology; D013045:Species Specificity; D015533:Transcriptional Activation
chemical_list: D017874:Immediate-Early Proteins