Rutaceae家族包括经济上重要的植物,因为它们在香料中的广泛应用,食物,油,医学,等。芦荟科植物能够通过生物技术更好地利用。现代生物技术方法主要依赖于功能蛋白在不同载体中的异源表达。然而,几种蛋白质很难在其天然环境之外表达。功能基因在异源系统中的表达潜力可以通过用功能基因的优选最佳密码子替换载体中的稀有同义密码子来最大化。密码子使用偏差在基于生物基因工程的研究和开发中起着至关重要的作用。在目前的研究中,分析了从10个Rutaceae植物家族成员的叶绿体基因组获得的727个编码序列(CDS)的密码子使用偏差。密码子的核苷酸组成分析表明,这些密码子富含A/T(U)碱基和优选的A/T(U)结尾。中立图的分析,有效密码子数(ENC)图,并对ENC与密码子适应指数(CAI)进行相关性分析,这揭示了自然选择是芦荟科植物家族密码子使用偏好的主要驱动力,其次是碱基突变。在ENC与CAI图,Rutaceae家族的密码子使用偏差与基因表达水平的关系可以忽略不计。对于每个样本,我们同时筛选了12个密码子作为首选密码子和高频密码子,其中GCU编码Ala,UUA编码Leu,编码Arg的AGA是最优选的密码子。一起来看,我们的研究揭示了菊科家族的同义密码子使用模式,为今后对芦荟科植物物种进行基因工程研究提供有价值的信息。
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes.
Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for
codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and
codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family\'s codon usage bias, followed by base mutation. In the ENC vs. CAI plot,
codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous
codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.