ALERT: This system is being upgraded on Tuesday December 12. It will not be available
for use for several hours that day while the upgrade is in progress. Deposits to DukeSpace
will be disabled on Monday December 11, so no new items are to be added to the repository
while the upgrade is in progress. Everything should be back to normal by the end of
day, December 12.
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
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 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.
Type
Journal articleSubject
AnimalsBirds
Brain
Comparative Genomic Hybridization
Contig Mapping
Gene Expression Profiling
Male
Models, Genetic
Mutation
Regression Analysis
Selection, Genetic
Sequence Alignment
Sequence Analysis, DNA
Sex Chromosomes
Permalink
https://hdl.handle.net/10161/11259Published Version (Please cite this version)
10.1111/j.1365-294X.2009.04487.xPublication Info
Künstner, 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.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item recordScholars@Duke
Erich David Jarvis
Adjunct Professor in the Deptartment 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 lear

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info