THE INFLUENCE OF SPECIFIC NEIGHBORING BASES ON SUBSTITUTION BIAS IN NONCODING REGIONS OF THE PLANT CHLOROPLAST GENOME

Substitutions occurring in noncoding sequences of the plant chloroplas t genome violate the independence of sites that is assumed by substitu tion models in molecular evolution. The probability that a substitutio n at a site is a transversion, as opposed to a transition, increases s ignificantly with increasing A + T content of the two adjacent nucleot ides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two featu res were examined; the influence of specific neighboring bases, as opp osed to the general A + T content, on transversion proportion and an i nfluence on substitutions by nucleotides other than the two immediatel y adjacent to the site of substitution. In both cases, a significant e ffect was found. In the case of specific nucleotides, transversion pro portion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. Th is specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the n ucleotides are ranked T > A > C > G as to their effect when they are i mmediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substit ution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclu sively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molec ular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies.