Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.

ABSTRACT: Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the 3 bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, among the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions: transversion bias. The data are consistent with a CpG effect, and it is shown that both the A + T content and the arrangement of purines/pyrimidines along the same DNA strand are correlated with rate variation. Expected equilibrium A + T content ranges from 36.4% to 82.8% across contexts, while G-C skew ranges from -77.4 to 72.2 and A-T skew ranges from -6

SUBMITTER: Morton BR 

PROVIDER: S-EPMC9339276 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature