Synonymous but not silent: functional codon bias reveals decoupled mitonuclear evolution in parasitic worms

Area of Science:

• Evolutionary Biology
• Genomics
• Parasitology

Background:

• Codon usage bias arises from a balance between mutational pressure and translational selection.
• The distinct evolutionary pressures on mitochondrial and nuclear genomes regarding codon bias are not fully understood.

Purpose of the Study:

• To comparatively analyze codon usage bias drivers in mitochondrial and nuclear genomes of parasitic helminths.
• To investigate the interplay of mutational and selection forces on synonymous codon usage in parasites.

Main Methods:

• Comparative genomic analysis of 120 parasitic helminths (Platyhelminthes and Nematoda).
• Integration of mitochondrial genome data with matched nuclear transcriptome data.
• Analysis of codon optimization patterns in relation to gene expression and functional importance (e.g., oxidative phosphorylation subunits).

Main Results:

• Mitochondrial genes show an AT-rich bias driven by mutational factors.
• Nuclear codon preferences correlate with gene expression, favoring optimal codons in highly expressed genes.
• Selection for codon optimization is evident in essential oxidative phosphorylation genes across both genomes, with variations indicating lineage-specific strategies.

Conclusions:

• Synonymous codon usage in parasites reflects functional adaptation relevant to parasite biology and control.
• Parasites exhibit diverse evolutionary strategies for respiratory system assembly, involving both mitonuclear coadaptation and compartmental decoupling.
• Understanding codon usage bias provides insights into parasite evolution and potential targets for control.