Journal Article

Patterns of Nucleotide Substitution Among Simultaneously Duplicated Gene Pairs in Arabidopsis thaliana

Liqing Zhang, Todd J. Vision and Brandon S. Gaut

in Molecular Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 19, issue 9, pages 1464-1473
Published in print September 2002 | ISSN: 0737-4038
Published online September 2002 | e-ISSN: 1537-1719 | DOI: https://dx.doi.org/10.1093/oxfordjournals.molbev.a004209

More Like This

Show all results sharing these subjects:

  • Evolutionary Biology
  • Molecular and Cell Biology

GO

Show Summary Details

Preview

We characterized rates and patterns of synonymous and nonsynonymous substitution in 242 duplicated gene pairs on chromosomes 2 and 4 of Arabidopsis thaliana. Based on their collinear order along the two chromosomes, the gene pairs were likely duplicated contemporaneously, and therefore comparison of genetic distances among gene pairs provides insights into the distribution of nucleotide substitution rates among plant nuclear genes. Rates of synonymous substitution varied 13.8-fold among the duplicated gene pairs, but 90% of gene pairs differed by less than 2.6-fold. Average nonsynonymous rates were ≈fivefold lower than average synonymous rates; this rate difference is lower than that of previously studied nonplant lineages. The coefficient of variation of rates among genes was 0.65 for nonsynonymous rates and 0.44 for synonymous rates, indicating that synonymous and nonsynonymous rates vary among genes to roughly the same extent. The causes underlying rate variation were explored. Our analyses tentatively suggest an effect of physical location on synonymous substitution rates but no similar effect on nonsynonymous rates. Nonsynonymous substitution rates were negatively correlated with GC content at synonymous third codon positions, and synonymous substitution rates were negatively correlated with codon bias, as observed in other systems. Finally, the 242 gene pairs permitted investigation of the processes underlying divergence between paralogs. We found no evidence of positive selection, little evidence that paralogs evolve at different rates, and no evidence of differential codon usage or third position GC content.

Journal Article.  7471 words.  Illustrated.

Subjects: Evolutionary Biology ; Molecular and Cell Biology