Codon degeneracy as well as pretermination codons influence transition to transversion ratio in coding sequences

Abstract

AbstractTransition to transversion ratio (ti/tv) is important in understanding the mutational bias in the evolution of an organism. Since synonymous polymorphism fortwo-fold degeneratecodons depends only on transitions, theti/tvratios oftwo-fold degeneratecodons andfour-fold degeneratecodons are expected to be different for synonymous as well as non-synonymous mutations. Therefore, in any organism, theti/tvratio is likely to vary among coding sequences having differences in degenerate codon composition. In addition to the above, compositional variation of pretermination codon among the coding sequences is also likely to influence theti/tvratio because purifying selection is stronger on non-synonymous substitutions leading to termination codons. In this study we have improved the method of finding the ratio between transition to transversion, synonymous transition to synonymous transversion and non-synonymous transition to non-synonymous transversion and developed a computational algorithm to calculate theti/tvvalues. Our analyses in 2516 coding sequences in theE. coligenome suggested a strong correlation of codon degeneracy with synonymous transition to transversion ratio. Additionally, we have observed a moderate correlation of pretermination codons with non-synonymous transition to transversion ratio. We believe that the improved method developed in this study can be potentially employed in finding theti/tvratio in coding sequences of other genomes.