Synonymous and non-synonymous transitions/transversions vividly disclose purifying selection inEscherichia colicoding sequences

Abstract

Transition to transversion ratio (ti/tv) is important in the study of molecular evolution, which provides the understanding of mutational bias in an organism. Since, synonymous polymorphism for two-fold degenerate codons depends only on transitions, two-fold degenerate codons and four-fold degenerate codons are different regarding (Ti/Tv) ratios both for synonymous as well as non-synonymous mutations. Therefore, various coding sequences in any organism having difference in degenerate codon composition is likely to affects the ti/tv ratio. In addition to the above, compositional differences among the coding sequences regarding pretermination codon is also likely to influence the ti/tv ratio because purifying selection is stronger on non-synonymous substitutions leading to termination codons. In this study we have improve the method of finding the ratio between transition to transversion, synonymous transition to synonymous transversion and non-synonymous transition to non-synonymous transversion and also developed a computer program to calculate the values. Our analyses in 2516 coding sequences in the E. coli genome suggested a strong correlation between codon degeneracy with synonymous transition to transversion ratio, also we have observed a moderate correlation between pretermination codons and non-synonymous transition to transversion. The percentage change between the conventional and improved method was the most striking part of our observation.