Codon usage bias and molecular evolution of Dnajc15 across avian lineages

Dnajc15, encoding the methylation-controlled J-protein (MCJ) of the HSP40 family, is an endogenous repressor of the mitochondrial respiratory chain and a key regulator of mitochondrial metabolism. The codon usage patterns and molecular evolution of Dnajc15 in birds remain largely uncharacterized.

We present the first systematic characterization of Dnajc15 codon usage patterns and adaptive evolution across 27 bird species representative of 11 avian orders, using codon usage bias analysis, PAML-based selection pressure analysis, and gene family analysis.

Codon usage bias analysis revealed a preference for A/U-ending codons and weak overall codon bias (effective codon number: 51.72-61.00). Selection analyses indicated predominant purifying selection (ω = 0.33). The M7 vs. M8 site model identified four candidate positively selected sites (positions 8, 17, 19, and 57), located in the N-terminal region and J-domain of the MCJ protein, though this signal was not corroborated by the M1a vs. M2a comparison, suggesting at most limited or episodic positive selection. Dnajc15 was retained across all examined vertebrate lineages despite widespread contraction of other Dnajc family members.

Dnajc15 is a highly conserved component of the avian mitochondrial regulatory system, with limited evidence for adaptive variation at a small number of candidate sites, consistent with strong long-term functional constraint.