Codon usage bias and selective constraints in Gentianales mitogenomes.

Area of Science:

• Evolutionary Biology
• Genomics
• Molecular Biology

Background:

• Mitochondrial genome evolution (MGE) in flowering plants is a complex process influenced by mutation, selection, and functional constraints.
• Understanding the interplay between intra- and inter-genomic factors driving MGE is crucial but challenging.

Purpose of the Study:

• To investigate the dynamics of MGE across twelve Gentianales species.
• To elucidate the distinct codon usage patterns and the evolutionary forces shaping them.

Main Methods:

• Analysis of codon usage patterns using ENc-GC3s plots, neutrality plots, and PR2 bias.
• Gene-specific analysis of substitution rates (dN, dS, dN/dS).
• Correlation analysis between codon biases, nucleotide composition, and evolutionary rates.

Main Results:

• Third codon positions exhibit significant variability (27.7% - 45.8%), indicating diverse selective pressures.
• Natural selection is the predominant force governing codon usage, outweighing mutational biases.
• Genes like atp, ccm, nad, and rps show signatures of positive selection, and third-codon biases optimize translation.

Conclusions:

• The study reveals a balance between mutation and selection in non-recombining mitochondrial genomes.
• Nucleotide composition influences synonymous substitution rates, offering insights into mitochondrial diversity in flowering plants.