Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

Authors

Errata

This article is corrected by:

  1. Errata: Corrigendum Volume 20, Issue 13, 2871, Article first published online: 6 June 2011

  • Axel Künstner’s PhD thesis focuses on molecular evolution of avian genomes. Research in the Ellegren laboratory integrates genomics and evolutionary biology.

Prof. Hans Ellegren, Fax: 0046 18 471 6310; E-mail: hans.ellegren@ebc.uu.se

Abstract

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 ∼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 (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill–Robertson effect (the effect of selection at linked loci) and point at stochastic problems with ω 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.

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