Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

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dc.contributor.author Santure, Anna en
dc.contributor.author Gratten, J en
dc.contributor.author Mossman, JA en
dc.contributor.author Sheldon, BC en
dc.contributor.author Slate, J en
dc.date.accessioned 2016-08-12T03:34:35Z en
dc.date.available 2011-06-02 en
dc.date.issued 2011-06-02 en
dc.identifier.citation BMC Genomics, 2011, 12 (1), 283 en
dc.identifier.uri http://hdl.handle.net/2292/29959 en
dc.description.abstract Background The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large phenotypic databases available for wild and non-model species, these data will provide an unprecedented opportunity to "genomicise" ecological model organisms and establish the genetic basis of quantitative traits in natural populations. Results This paper describes the sequencing, de novo assembly and analysis from the transcriptome of eight tissues of ten wild great tits. Approximately 4.6 million sequences and 1.4 billion bases of DNA were generated and assembled into 95,979 contigs, one third of which aligned with known Taeniopygia guttata (zebra finch) and Gallus gallus (chicken) transcripts. The majority (78%) of the remaining contigs aligned within or very close to regions of the zebra finch genome containing known genes, suggesting that they represented precursor mRNA rather than untranscribed genomic DNA. More than 35,000 single nucleotide polymorphisms and 10,000 microsatellite repeats were identified. Eleven percent of contigs were expressed in every tissue, while twenty one percent of contigs were expressed in only one tissue. The function of those contigs with strong evidence for tissue specific expression and contigs expressed in every tissue was inferred from the gene ontology (GO) terms associated with these contigs; heart and pancreas had the highest number of highly tissue specific GO terms (21.4% and 28.5% respectively). Conclusions In summary, the transcriptomic data generated in this study will contribute towards efforts to assemble and annotate the great tit genome, as well as providing the markers required to perform gene mapping studies in wild populations. en
dc.description.uri http://www.ncbi.nlm.nih.gov/pubmed/21635727 en
dc.language English en
dc.publisher BioMed Central Ltd en
dc.relation.ispartofseries BMC Genomics en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from http://www.sherpa.ac.uk/romeo/issn/1471-2156/ http://www.biomedcentral.com/about/open-access en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri https://creativecommons.org/licenses/by/2.0/ en
dc.title Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing en
dc.type Journal Article en
dc.identifier.doi 10.1186/1471-2164-12-283 en
pubs.issue 1 en
pubs.volume 12 en
dc.description.version VoR - Version of Record en
dc.identifier.pmid 21635727 en
pubs.author-url http://www.biomedcentral.com/1471-2164/12/283 en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Article en
pubs.elements-id 417094 en
pubs.org-id Science en
pubs.org-id Biological Sciences en
dc.identifier.eissn 1471-2164 en
pubs.number 283 en
pubs.record-created-at-source-date 2013-12-09 en
pubs.dimensions-id 21635727 en


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