Patterns of codon usage in plastidial genomes of ancient plants provide insights into evolution

Abstract

Basal angiosperms are the first flowering plants that diverged from ancestral angiosperms, while magnoliids represent the oldest known angiosperms and are considered to retain the characteristics of more primitive angiosperms. Availability of the plastidial genomes from several members of both these classes of plants provides an opportunity to identify and understand large-scale genomic patterns in organelles of early angiosperms. In this work, chloroplast genomes from nine AT-rich basal angiosperm and magnoliid species were analyzed to unearth patterns, if any, in terms of codon bias and to identify factors responsible for the detected patterns. We were able to distinguish nine optimal codons in basal angiosperm chloroplasts and 18 in case of magnoliids. Our findings suggest mutational bias as the most predominant factor shaping codon usage patterns among the genomes examined, while gene expression, hydrophobicity and aromaticity, were found to have a limited but important effect on pattern determination.