Abstract
The influence of neighboring base composition, or context, on substitution bias at fourfold degenerate coding sites and in intergenic regions in plastid DNA is compared across the angiosperms, gymnosperms, ferns, liverworts, chlorophytes, stramenopiles and rhodophytes. An influence of flanking base G + C content on the relative rates of transitions and transversions is observed in all lineages and extends up to four nucleotides from the site of substitution in some. Despite finding context effects in all lineages, significant differences were observed between lineages. Overall, the data suggest that context is a general factor affecting mutation bias in plastid DNA but that the dynamics of the influence have evolved over time. It is also shown that, although there are similar effects of context on substitution bias at fourfold degenerate coding sites and at sites within intergenic regions, there are also small but significant differences, suggesting that there could be some selection on some of these sites and that there could be some difference in the mutation and/or repair process between coding and noncoding DNA.
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The data underlying this article will be shared on reasonable request to the corresponding author.
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The author would like to thank Gavin Huttley for useful comments and ideas on an earlier version of this manuscript.
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Handling editor: Michelle Meyer.
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Supplementary file1 Supplemental Fig. S1. Transition and transversion rate variation across N1 contexts in (a) coding and (b) noncoding DNA. Black bars show the difference in the transitions/site between the N1 = 2 and N1 = 0 contexts while open bars show the difference in transversions/site between these contexts. Supplemental Fig. S2. Transition:transversion across N1 G+C contexts in the Ulvophyceae (striped) and Chlorophyceae (open) (DOCX 8369 kb)
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Morton, B.R. Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups. J Mol Evol 90, 44–55 (2022). https://doi.org/10.1007/s00239-021-10040-2
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DOI: https://doi.org/10.1007/s00239-021-10040-2