Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E Mach 1, 38010 S. Michele all'Adige (TN), Italy.
Genomics. 2013 May;101(5):290-5. doi: 10.1016/j.ygeno.2013.02.008. Epub 2013 Mar 6.
We conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis presented in our study suggests a correlation, which is negative but highly correlated between Axis 1 and GC3s (r=-0.827, P<0.01), indicating that mutational bias has a significant and dominant repressive role to the choices of GC3. We also observed a strong positive correlation between codon adaptation index (CAI) and translational adaptation index (tAIg) (0.407, P<0.01), which demonstrates the facilitation of efficient translation by the optimal codon usage patterns of the highly expressed genes. We believe that the complete set of optimal codon usage patterns detected in this study will serve as a model to enhance the transgenesis in the studied cultivar of Solanum lycopersicum.
我们基于栽培品种 Micro-Tom 的非冗余全长 cDNA（nrFLcDNA）和表达序列标签（EST）数据，进行了全面的密码子使用偏性（CUB）分析，并评估了观察到的 CUB 与转录和翻译效率测量之间的关联。我们的研究结果表明，轴 1 和 GC3s 之间存在负相关但高度相关的关系（r=-0.827，P<0.01），这表明突变偏向对 GC3 的选择具有显著的抑制作用。我们还观察到密码子适应指数（CAI）和翻译适应指数（tAIg）之间存在很强的正相关关系（0.407，P<0.01），这表明高效翻译受到高度表达基因的最优密码子使用模式的促进。我们相信，本研究中检测到的完整最优密码子使用模式集将作为提高研究栽培番茄 Lycopersicon esculentum 中转基因效率的模型。
