Journal
MOLECULAR ECOLOGY
Volume 19, Issue -, Pages 266-276Publisher
WILEY
DOI: 10.1111/j.1365-294X.2009.04487.x
Keywords
Next generation sequencing; 454; Avian genomics; Male-mutation bias; Selection; Hill-Robertson effect
Funding
- NSF [IBN-0646459]
- National Science Foundation [MCB-0817687]
- NIH [5F32GPM072494]
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0815354, 0817687] Funding Source: National Science Foundation
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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 similar to 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.
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