TITLE

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

AUTHOR(S)
Replogle, Kirstin; Arnold, Arthur P.; Ball, Gregory F.; Band, Mark; Bensch, Staffan; Brenowitz, Eliot A.; Shu Dong; Drnevich, Jenny; Ferris, Margaret; George, Julia M.; Gong, George; Hasselquist, Dennis; Hernandez, Alvaro G.; Kim, Ryan; Lewin, Harris A.; Lei Liu; Lovell, Peter V.; Mello, Claudio V.; Naurin, Sara; Rodriguez-Zas, Sandra
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
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.
ACCESSION #
38122702

 

Related Articles

  • Genomic organization of zebra finch alpha and beta globin genes and their expression in primitive and definitive blood in comparison with globins in chicken. Alev, Cantas; Shinmyozu, Kaori; McIntyre, Brendan A. S.; Sheng, Guojun // Development Genes & Evolution;Jul2009, Vol. 219 Issue 7, p353 

    How alpha and beta globin genes are organized and expressed in amniotes is of interest to researchers in a wide variety of fields. Data regarding this from avian species have been scarce. Using genomic and proteomic approaches, we present here our analysis of alpha and beta globins of zebra...

  • Impact of GC content on gene expression pattern in chicken. You Sheng Rao; Xue Wen Chai; Zhang Feng Wang; Qing Hua Nie; Xi Quan Zhang // Genetics Selection Evolution;Apr2013, Vol. 45 Issue 4, p1 

    Background: GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and...

  • Digital gene expression analysis of the zebra finch genome. Ekblom, Robert; Balakrishnan, Christopher N.; Burke, Terry; Slate, Jon // BMC Genomics;2010, Vol. 11, p219 

    Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel...

  • Songbird genome gives insight into memory and speech.  // Australian Life Scientist;4/1/2010, p2 

    The genome of the zebra finch is helping us understand how we learn how to speak.

  • IN BRIEF.  // Nature Reviews Genetics;Apr2001, Vol. 2 Issue 4, p242 

    Presents an update on studies regarding genetics and genomics as of April 2001. Gene predictions in Caenorhabditis elegans; Evolution of the gene complex S, in the Brassica species; Expression profiling using the RIKEN set of full-length enriched mouse complementaryDNA arrays.

  • Potential roles of antisense technology in cancer chemotherapy. Crooke, Stanley T // Oncogene;12/27/2000 Review, Vol. 19 Issue 56, p6651 

    Antisense technology may play a major role in cancer chemotherapy. It is clearly a tool of exceptional value in the functionalization of genes and their validation as potential targets for cancer chemotherapy. Additionally, there is now substantial evidence that antisense drugs are safe, and a...

  • A method for detecting and correcting feature misidentification on expression microarrays. I-Ping Tu; Schaner, Marci; Diehn, Maximilian; Sikic, Branimir I.; Brown, Patrick O.; Botstein, David; Fero, Michael J. // BMC Genomics;2004, Vol. 5, p64 

    Background: Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and at the Stanford Functional Genomics Facility (SFGF). Nevertheless, as large datasets based on the...

  • Microarrays Demystified. Medlin, Jennifer // Environmental Health Perspectives;Mar2004, Vol. 112 Issue 4, pA222 

    Reports on the use of microarray chips to analyze the changing patterns of gene expression across the entire genome. Introduction of liquid-handling robotics; Inclusion of fluorescent-labeled complementary DNA (cDNA) groups that contain spots of gene fragments complementary to the labeled cDNA;...

  • Making sense of EST sequences by CLOBBing them. Parkinson, John; Guiliano, David B.; Blaxter, Mark // BMC Bioinformatics;2002, Vol. 3, p31 

    Background: Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to sequencing errors and typically define incomplete transcripts. To increase the...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics