Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains

密码子使用偏好性 生物 遗传学 线粒体DNA 基因组 基因
作者
Wei Gao,Xiaodie Chen,Jing He,Ajia Sha,Yingyong Luo,Wenqi Xiao,Zhuang Xiong,Qiang Li
出处
期刊:BMC Genomics [Springer Nature]
卷期号:25 (1) 被引量:9
标识
DOI:10.1186/s12864-024-10374-3
摘要

Abstract In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species. The results revealed that the codons of all Pleurotus strains had a preference for ending in A/T. Furthermore, the correlation between codon base compositions and codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) indices was also detected, implying the influence of base composition on codon bias. The two P. ostreatus species were found to have differences in various base bias indicators. The average effective number of codons (ENC) of mitochondrial core PCGs of Pleurotus was found to be less than 35, indicating strong codon preference of mitochondrial core PCGs of Pleurotus . The neutrality plot analysis and PR2-Bias plot analysis further suggested that natural selection plays an important role in Pleurotus codon bias. Additionally, six to ten optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified in eight Pleurotus strains, with UGU and ACU being the most widely used optimal codons in Pleurotus . Finally, based on the combined mitochondrial sequence and RSCU value, the genetic relationship between different Pleurotus strains was deduced, showing large variations between them. This research has improved our understanding of synonymous codon usage characteristics and evolution of this important fungal group.
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