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

Synonymous codon usage reflects a balance between intrinsic mutational pressures and extrinsic translational selection, yet how these forces interact across genomic compartments remains poorly resolved. Here, we perform a comparative analysis of 120 parasitic helminths (Platyhelminthes and Nematoda), integrating mitochondrial genomes with matched nuclear transcriptomes to dissect the drivers of codon bias. Mitochondrial genes exhibit a strong AT-rich signature consistent with strand-asymmetric mutational bias, but also reveal lineage-specific departures reflecting translational optimization. In contrast, nuclear codon preferences correlate with gene expression, with highly expressed mitochondrial genes preferentially employing optimal codons to enhance translational efficiency. Across both compartments, ENc–GC3s patterns consistently fall below neutrality expectations, indicating pervasive selection beyond drift. At the functional level, codon adaptation is concentrated in core oxidative phosphorylation subunits (e.g., COX1, COX2), whereas accessory genes such as ATP8 display relaxed bias, revealing fine-scale differentiation of translational demands. Comparative analyses further uncover both mitonuclear coadaptation and, in some lineages, compartmental decoupling, highlighting divergent evolutionary strategies. By demonstrating that synonymous codons are neither silent nor random, but encode functional mitonuclear adaptation, this study provides a general framework for codon usage evolution across metazoans and opens new perspectives on host adaptation and parasite control.