Key Laboratory for Specialty Agricultural Germplasm Resources Development and Utilization of Guizhou Province, Liupanshui Normal University, Liupanshui 553004, China.
Genes (Basel). 2024 Jul 9;15(7):899. doi: 10.3390/genes15070899.
var. , a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of var. . The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of var. was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of var. .
变叶木，一种属于蔷薇科的矮小灌木，原产于亚洲，其光合作用对温度变化具有显著的可塑性。然而，该物种叶绿体基因组中的密码子使用模式及其影响因素尚未有文献记载。本研究对 var. 进行了全基因组测序和组装。利用 CodonW 1.4.2 软件，通过多变量统计方法（包括中性作图、PR2 偏性作图和有效密码子数 (ENC) 作图）分析叶绿体基因组中注释基因的密码子组成。结果表明，53 个 CDS 的平均 GC 含量为 38.08%，第三密码子碱基位置的平均 GC 含量为 27.80%，表明叶绿体基因在第三密码子位置偏好 A/U(T)。此外，叶绿体基因表现出较弱的整体密码子使用偏性（CUB），根据 ENC 值和其他指标。相关性分析表明，ENC 值与 GC2 呈显著负相关，与 GC3 呈极显著正相关，与 GC1 含量无相关性。这些发现强调了第三位置密码子组成对影响密码子使用偏性的重要性。此外，我们的分析表明，var. 叶绿体基因组的 CUB 主要受自然选择和其他因素的影响。最后，本研究确定了 UCA、CCU、GCU、AAU、GAU 和 GGU 为最优密码子。这些结果为 var. 叶绿体基因组的遗传修饰和进化动态提供了基础认识。
