THE INFLUENCE OF NEIGHBORING BASE COMPOSITION ON SUBSTITUTIONS IN PLANT CHLOROPLAST CODING SEQUENCES

The bias of nucleotide substitutions in noncoding sequences of the pla nt chloroplast genome is strongly dependent on the composition of the two flanking bases. Substitutions in G+C-rich environments have a stro ng bias toward transitions, while in AST-rich environments, transversi ons outnumber transitions. In this study, the correlation between the composition of neighboring bases and nucleotide substitution bias is e xamined in a variety of coding sequences in the plant chloroplast geno me. The analyses include both multiple sequence alignments, for the rb cL and ndhF genes, and a pairwise comparison of rice and maize for 22 chloroplast genes. Substitution bias, measured in terms of transversio n proportion, is found to be significantly correlated with the composi tion of the two neighboring bases, as in noncoding sequences. However, the influence of the two neighboring bases on substitutions in the rb cL gene is different than what is observed in ndhF and other coding se quences, where context dependency is the same as in noncoding sequence s. This difference is examined and appears to be the result of an infl uence of nucleotides other than the two immediate neighbors on substit ution bias in conjunction with a lower overall A+T content in the rbcL gene. The results indicate that the synonymous substitution process i n the chloroplast genome is strongly context dependent in a complex ma nner.