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

## TL;DR

This paper studies how codon usage differs between a parasitic fungus and its insect host, revealing how genetic factors might contribute to their specific relationship.

## Contribution

The study reveals co-adaptation in codon usage between a parasitic fungus and its host, offering new molecular insights into obligate parasitism.

## Key findings

- Codon usage in nuclear genes is shaped by natural selection, while mitochondrial genes are influenced by mutational pressure.
- Overlap in optimal codons for certain amino acids suggests gene-expression level co-adaptation between the fungus and its host.
- Nuclear genomes of O. sinensis and T. xiaojinensis show contrasting GC-ending codon preferences.

## Abstract

Ophiocordyceps sinensis, a rare medicinal fungus endemic to the Qinghai–Tibet Plateau, exhibits a highly specific obligate parasitic relationship with its insect host, Thitarodes xiaojinensis. To investigate potential genetic underpinnings of this specificity, we analyzed codon usage bias in both the nuclear and mitochondrial genomes of the fungus and its host. The results indicate that codon usage in both organisms is shaped by both natural selection and mutational pressure. The nuclear genes are primarily driven by natural selection, whereas the mitochondrial genes are more influenced by mutational pressure. Notably, overlap in optimal codons for certain amino acids suggests possible co-adaptation at the gene-expression level. This study provides molecular evolutionary insights into the adaptation mechanisms of O. sinensis and its host, offering new perspectives on the evolution of obligate parasitism and a theoretical basis for future cultivation and conservation efforts.

Ophiocordyceps sinensis, 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 O. sinensis and Thitarodes xiaojinensis was explored by analyzing the nuclear genomes and mitochondrial genomes of the two. The nuclear genomes showed contrasting preferences: O. sinensis sclerotium exhibited strong GC-ending codon bias (GC3 = 66.13%), while T. xiaojinensis 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 O. sinensis and 28 (GC-ending) in T. xiaojinensis 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 O. sinensis and T. xiaojinensis 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.