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

Publication ,  Journal Article
Künstner, A; Wolf, JBW; Backström, N; Whitney, O; Balakrishnan, CN; Day, L; Edwards, SV; Janes, DE; Schlinger, BA; Wilson, RK; Jarvis, ED ...
Published in: Mol Ecol
March 2010

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.

Duke Scholars

Published In

Mol Ecol

DOI

EISSN

1365-294X

Publication Date

March 2010

Volume

19 Suppl 1

Issue

Suppl 1

Start / End Page

266 / 276

Location

England

Related Subject Headings

  • Sex Chromosomes
  • Sequence Analysis, DNA
  • Sequence Alignment
  • Selection, Genetic
  • Regression Analysis
  • Mutation
  • Models, Genetic
  • Male
  • Gene Expression Profiling
  • Evolutionary Biology
 

Citation

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Künstner, A., Wolf, J. B. W., Backström, N., Whitney, O., Balakrishnan, C. N., Day, L., … Ellegren, H. (2010). Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol, 19 Suppl 1(Suppl 1), 266–276. https://doi.org/10.1111/j.1365-294X.2009.04487.x
Künstner, Axel, Jochen B. W. Wolf, Niclas Backström, Osceola Whitney, Christopher N. Balakrishnan, Lainy Day, Scott V. Edwards, et al. “Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.Mol Ecol 19 Suppl 1, no. Suppl 1 (March 2010): 266–76. https://doi.org/10.1111/j.1365-294X.2009.04487.x.
Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, et al. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 2010 Mar;19 Suppl 1(Suppl 1):266–76.
Künstner, Axel, et al. “Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.Mol Ecol, vol. 19 Suppl 1, no. Suppl 1, Mar. 2010, pp. 266–76. Pubmed, doi:10.1111/j.1365-294X.2009.04487.x.
Künstner A, Wolf JBW, Backström N, Whitney O, Balakrishnan CN, Day L, Edwards SV, Janes DE, Schlinger BA, Wilson RK, Jarvis ED, Warren WC, Ellegren H. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol. 2010 Mar;19 Suppl 1(Suppl 1):266–276.
Journal cover image

Published In

Mol Ecol

DOI

EISSN

1365-294X

Publication Date

March 2010

Volume

19 Suppl 1

Issue

Suppl 1

Start / End Page

266 / 276

Location

England

Related Subject Headings

  • Sex Chromosomes
  • Sequence Analysis, DNA
  • Sequence Alignment
  • Selection, Genetic
  • Regression Analysis
  • Mutation
  • Models, Genetic
  • Male
  • Gene Expression Profiling
  • Evolutionary Biology