Song Yuxuan, Shen Meng, Cao Fuliang, Yang Xiaoming
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Int J Mol Sci. 2024 Dec 24;26(1):39. doi: 10.3390/ijms26010039.
Codon usage bias (CUB) refers to the different frequencies with which various codons are utilized within a genome. Examining CUB is essential for understanding genome structure, function, and evolution. However, little was known about codon usage patterns and the factors influencing the nuclear genomes of eight ecologically significant Sapindaceae species widely utilized for food and medicine. In this study, an analysis of nucleotide composition revealed a higher A/T content and showed a preference for A/T at the third codon position in the eight species of Sapindaceae. A correspondence analysis of relative synonymous codon usage explained only part of the variation, suggesting that not only natural selection but also various other factors contribute to selective constraints on codon bias in the nuclear genomes of the eight Sapindaceae species. Additionally, ENC-GC3 plot, PR2-Bias, and neutrality plot analyses indicated that natural selection exerted a greater influence than mutation pressure across these eight species. Among the eight Sapindaceae species, 16 to 26 optimal codons were identified, with two common high-frequency codons: AGA (encoding Arg) and GCU (encoding Ala). The clustering heat map, which included the 8 Sapindaceae species and 13 other species, revealed two distinct clusters corresponding to monocots and dicots. This finding suggested that CUB analysis was particularly effective in elucidating evolutionary relationships at the family level. Collectively, our results emphasized the distinct codon usage characteristics and unique evolutionary traits of the eight Sapindaceae species.
密码子使用偏好（CUB）是指基因组中各种密码子被使用的频率不同。研究CUB对于理解基因组结构、功能和进化至关重要。然而，对于广泛用于食品和医药的八种具有重要生态意义的无患子科物种的密码子使用模式以及影响其核基因组的因素知之甚少。在本研究中，核苷酸组成分析显示这八种无患子科物种的A/T含量较高，并且在第三密码子位置偏好A/T。相对同义密码子使用的对应分析仅解释了部分变异，这表明不仅自然选择，还有各种其他因素对这八种无患子科物种核基因组中的密码子偏好施加了选择性限制。此外，ENC-GC3图、PR2偏差和中性图分析表明，在这八个物种中自然选择比突变压力的影响更大。在这八种无患子科物种中，鉴定出了16至26个最优密码子，其中有两个常见的高频密码子：AGA（编码精氨酸）和GCU（编码丙氨酸）。包含这8种无患子科物种和其他13个物种的聚类热图显示出对应单子叶植物和双子叶植物的两个不同聚类。这一发现表明，CUB分析在阐明科级水平的进化关系方面特别有效。总体而言，我们的结果强调了这八种无患子科物种独特的密码子使用特征和独特的进化特性。
