Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
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Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.
Comparative Genomic Hybridization
Gene Expression Profiling
Sequence Analysis, DNA
Published Version (Please cite this version)10.1111/j.1365-294X.2009.04487.x
Publication InfoKünstner, Axel; Wolf, Jochen BW; Backström, Niclas; Whitney, Osceola; Balakrishnan, Christopher N; Day, Lainy; ... Ellegren, Hans (2010). Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol, 19 Suppl 1. pp. 266-276. 10.1111/j.1365-294X.2009.04487.x. Retrieved from https://hdl.handle.net/10161/11259.
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Adjunct Professor in the Dept. of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. They use an integrative approach that combines behavioral, anatomical, electrophysiological and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The generality of the discoveries is tested in other vocal