Jarvis lab 454 data
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
We sequenced 2.5 plates of brain transcriptome data from multiple bird species using 454 FLX-GS platform. To analyze 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 6,499 different genes across all 10 species, with approximately 1,000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems 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 genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.