AUTHOR=Wu Peng , Xiao Wenqi , Luo Yingyong , Xiong Zhuang , Chen Xiaodie , He Jing , Sha Ajia , Gui Mingying , Li Qiang 

TITLE=Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1170790

DOI=10.3389/fmicb.2023.1170790

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p>Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of <italic>Ganoderma</italic> species remain unknown.</p></sec><sec><title>Methods</title><p>In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 <italic>Ganoderma</italic> species, including 13 <italic>Ganoderma</italic> strains.</p></sec><sec><title>Results</title><p>The codons of all <italic>Ganoderma</italic> strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within <italic>Ganoderma</italic> strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of <italic>Ganoderma</italic> have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in <italic>Ganoderma</italic>. Additionally, 11 to 22 optimal codons (ΔRSCU&gt;0.08 and RSCU&gt;1) were identified in 13 <italic>Ganoderma</italic> strains, with GCA, AUC, and UUC being the most widely used optimal codons in <italic>Ganoderma</italic>. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within <italic>Ganoderma</italic> strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain <italic>Ganoderma</italic> species.</p></sec><sec><title>Discussion</title><p>This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.</p></sec>