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Digital gene expression analysis of the zebra finch genome

Ekblom, R., Balakrishnan, C.N., Burke, T. and Slate , J. (2010) Digital gene expression analysis of the zebra finch genome. BMC Genomics, 11. Art no.219. ISSN 1471-2164

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Abstract

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 sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC).

Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function.

Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates.

Item Type: Article
Copyright, Publisher and Additional Information: © 2010 Ekblom et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Major Histocompatibility Complex; Housekeeping Genes; Taeniopygia-Guttata; Darwinian Selection; Evolution; Transcriptome; MHC; Drosophila; Sequence; Divergence
Institution: The University of Sheffield
Academic Units: The University of Sheffield > Faculty of Science (Sheffield) > School of Biological Sciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield)
Depositing User: Miss Anthea Tucker
Date Deposited: 07 May 2010 10:01
Last Modified: 12 Jun 2014 02:19
Published Version: http://dx.doi.org/10.1186/1471-2164-11-219
Status: Published
Publisher: BioMed Central
Identification Number: 10.1186/1471-2164-11-219
URI: http://eprints.whiterose.ac.uk/id/eprint/10811

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