Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, School of Forestry, Hainan University, Haikou 570228, China.
Genes (Basel). 2023 May 19;14(5):1110. doi: 10.3390/genes14051110.
The plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of , we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of , providing new insights into codon biology and the evolution of plants.
该植物广泛分布于 130 多个热带和亚热带国家，具有重要的经济和药用价值。密码子使用偏性（CUB）是研究基因功能和进化的关键特征，它可以更好地理解生物基因调控。在这项研究中，我们全面分析了核基因组、叶绿体基因组和基因表达的 CUB 模式，以及物种的系统进化。结果表明，和的核基因组和叶绿体基因组编码区的同义密码子和最优密码子偏好以 A/U 结尾于第三位碱基。自然选择是影响 CUB 特征的主要因素。此外，在高表达的基因中，我们发现具有较强 CUB 的基因表达水平更高，这些高表达基因倾向于使用 G/C 结尾的密码子。此外，系统树中蛋白编码序列和叶绿体基因组序列的分支模式非常相似，与叶绿体基因组 CUB 的聚类不同。本研究强调了不同基因组中物种的 CUB 模式和特征，探讨了 CUB 偏好与基因表达的相关性，并进一步研究了物种的系统进化，为密码子生物学和植物的进化提供了新的见解。
