Journal Article

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Robert Ekblom, Lisa French, Jon Slate and Terry Burke

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 781-790
Published in print January 2010 |
Published online September 2010 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evq061

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Genes of the immune system are generally considered to evolve rapidly due to host–parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated dN/dS ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher dN/dS ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds.

Keywords: genomics; bird; immunogenetics; next-generation sequencing; digital transcriptomics; Taeniopygia guttata

Journal Article.  6305 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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