@article {RN135, title = {Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. (vol 19, pg 266, 2010)}, journal = {Molecular Ecology}, volume = {20}, year = {2011}, pages = {2871-2871}, type = {Journal Article}, 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 (
d
S
) and
chromosome size. Analyses of the mean
d
N
/
d
S
ratio (
ω
) of genes across chromosomes supported the
Hill{\textendash}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

}, issn = {0962-1083}, doi = {10.1111/j.1365-294X.2011.05169.x}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904817/}, author = {Kuenstner, A. and Wolf, J. B. W. and Backstroem, N. and Whitney, O. and Balakrishnan, C. N. and Day, L. and Edwards, S. V. and Janes, D. E. and Schlinger, B. A. and Wilson, R. K. and Jarvis, E. D. and Warren, W. C. and Ellegren, H.} }