New insights into the interplay between codon bias determinants in plants

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Codon bias, the non-random usage of synonymous codons, is observed across diverse species.
• Potential drivers include neutral mechanisms (mutation, gene conversion, drift) and selection (mRNA stability, translation efficiency, accuracy).
• The relative contributions of these factors to codon bias remain unclear.

Purpose of the Study:

• To dissect the contributions of mutational bias and selection to codon bias in plant genes.
• To analyze genomic composition and its influence on codon usage profiles.
• To compare codon bias patterns between monocots, dicots, and mosses.

Main Methods:

• Analysis of mononucleotide, dinucleotide, and trinucleotide frequencies in plant genes.
• Investigation of genomic compositional background.
• Comparative analysis across 15 eudicots, 4 monocots, and 2 mosses.

Main Results:

• Neutral forces, particularly mutational pressure and G|C-biased gene conversion, explain most observed codon bias.
• Evidence suggests selection for translational efficiency and mRNA folding also plays a role.
• Monocots exhibit lower background compositional bias but higher overall codon bias than dicots.

Conclusions:

• Neutral evolutionary forces are the predominant drivers of codon bias in the studied plant species.
• Selection contributes to codon usage optimization, influencing translational efficiency and mRNA structure.
• Significant compositional differences exist between monocots and dicots, impacting their codon bias patterns.