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http://dx.doi.org/10.5352/JLS.2010.20.4.481

The Rates of Synonymous and Nonsynonymous Substitutions in Sorbus aucuparia Using Nuclear and Chloroplast Genes  

Huh, Man-Kyu (Department of Molecular Biology, Dongeui University)
Publication Information
Journal of Life Science / v.20, no.4, 2010 , pp. 481-486 More about this Journal
Abstract
The rates of synonymous and nonsynonymous nucleotide substitutions were studied for sequences of nuclear and chloroplast genes in Sorbus aucuparia. Results suggested that DNA evolution in this species had taken place, on average, at a slower rate in the chloroplast genes than in the nuclear genes: a rate variation pattern similar to those observed in eudicot plants. Within the nucleus, the synonymous substitution rates (Ks) (2.45-2.60) were two-fold higher than nonsynonymous substitution rates (Ka) (1.15-1.30). More notably, the values of Ks (1.20-1.26) were about six-fold higher than those of Ka (0.26-0.42) within the chloroplast genome. Ka/Ks ratios for nuclear and chloroplast genes of S. aucuparia had mean values of 0.178 and 0.056, respectively. A Ka/Ks ratio < 1 indicated negative (purifying) selection. The chloroplast genes had a lower effective number of codons (ENC) values (22.4-32.2) than those of nuclear genes (35.8-38.7). The analysis of the G+C content indicated that the chloroplast genes in this investigation had a higher preference for synonymous codons ending with A and T (G+C content range, 28.4-29.1%) where there was a slight bias toward codons ending with G+C (63.2-64.2%) in the nuclear genome.
Keywords
Sorbus aucuparia; nuclear genes; chloroplast genes; synonymous; nonsynonymous;
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