Analysis of codon usage bias between Ophiocordyceps sinensis and Thitarodes xiaojinensis

Abstract Background Ophiocordyceps sinensis is a well - known entomogenous fungus, which has attracted much attention due to its unique medicinal value and complex ecological relationships. Thitarodes xiaojinensis is one of the main hosts of the Ophiocordyceps sinensis fungus, and a typical parasitic symbiotic relationship has formed between the two. To investigate whether the codon usage preferences of O. sinensis and T. xiaojinensis are related to the parasitic relationship between them, a systematic analysis of the codon usage patterns of nuclear genes and mitochondrial genes in these two organisms was conducted. Results The GC content at the third position of codons in the nuclear genome of O. sinensis sclerotium was 66.13%, indicating a strong preference for codons ending with G or C. The GC content at the third position of codons in the nuclear genome of T. xiaojinensis was 49.14%, indicating a strong preference for codons ending with A or T. In the mitochondrial genomes, the content of A or T at the 3rd position of the codons of both is higher than 70%, showing a strong preference for T and A. There are 25 and 28 optimal codons in the nuclear genomes of O. sinensis and T. xiaojinensis respectively, and both end with G or C; there are 16 and 13 optimal codons in the mitochondrial genomes of O. sinensis and T. xiaojinensis respectively, and both end with A or T. Through the analysis of the nuclear genome, it was found that there were overlaps of two or more optimal codons for amino acids such as Leucine (Leu), Valine (Val), Serine (Ser), and Proline (Pro) between O. sinensis and T. xiaojinensis . In the mitochondrial genome, there was only an overlap of one optimal codon for amino acids such as Phenylalanine (Phe), Leucine (Leu), Aspartic acid (Asp), and Serine (Ser). Neutral plotting analysis, ENC analysis, RSCU analysis, and parity bias analysis show 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. Coclusions: Among them, natural selection is the main influencing factor for the nuclear genomes of O. sinensis and T. xiaojinensis , while mutation pressure is the main influencing factor for the mitochondrial genome of O. sinensis and the mitochondrial genome of T. xiaojinensis . By analyzing the nuclear genes and mitochondrial genes of the O. sinensis and T. xiaojinensis ,a new insights are provided into the parasitic relationship and host specificity between O. sinensis and T. xiaojinensis .