Analysis of Codon Usage Bias Between Entomopathogenic Fungus Ophiocordyceps sinensis and Its Host, Thitarodes xiaojinensis

<i>Ophiocordyceps sinensis</i>, a fungus parasitic on insects, attracts interest due to its unique medicinal applications and complex ecological interactions. The potential relationship between codon usage bias and the parasitic relationship between <i>O. sinensis</i> and <i>Thitarodes xiaojinensis</i> was explored by analyzing the nuclear genomes and mitochondrial genomes of the two. The nuclear genomes showed contrasting preferences: <i>O. sinensis</i> sclerotium exhibited strong GC-ending codon bias (GC3 = 66.13%), while <i>T. xiaojinensis</i> favored AT-ending codons (GC3 = 49.14%). Conversely, both mitochondrial genomes displayed a strong preference (>70% AT) for AT-ending codons. Optimal codon analysis revealed 25 (GC-ending) in <i>O. sinensis</i> and 28 (GC-ending) in <i>T. xiaojinensis</i> nuclear genomes, with overlaps for Leu, Val, Ser, and Pro. The mitochondrial genomes had fewer optimal codons (16 and 13, AT-ending), showing limited overlap (Phe, Leu, Asp, Ser). Neutral plotting analysis, effective number of codons analysis, relative synonymous codon usage analysis, and parity bias analysis showed that the codon usage preferences of the nuclear genomes and mitochondrial genomes of <i>O. sinensis</i> and <i>T. xiaojinensis</i> are jointly affected by selection and mutation pressure. Natural selection predominates in nuclear genomes, while mutation pressure dominates in mitochondrial genomes. This provides new molecular insights into their host-parasite specificity.