为了揭示花分生组织决定基因AP1 (APETALA1)的分子机制以及物种间的进化关系,从GenBank数据库挑选8个不同植物AP1基因编码序列,利用R软件分别计算GC含量、有效密码子数(Effective number of codons,ENC)、同义密码子相对使用度(Relative synonymous codon usage,RS CU)、相对密码子使用偏好性(Relative codon usage bias,RCBS)等参数,分析比较不同植物AP1基因密码子使用模式中密码子偏好性和碱基组成动力学.结果表明,不同植物AP1基因密码子使用受到GC偏好性(GC bias)影响,特别是GC3s;大多数最优密码子偏好使用以A/U结尾,其中不同植物AP1基因中ACA、AUA和CAG均表现为较高的RSCU值,为最优势密码子;芍药(Paeonia lactiflora)和牡丹(Paeonia suuticosa)AP1基因的密码子使用特点相似,碧桃(Prunus persica)和苹果(Malus×domestica)相似;较低的最优密码子频率Fop值和较高的ENC值暗示了不同植物AP1基因在密码子使用中具有一个较弱的偏好性.
Comparative Analysis of Codon Usage Patterns in APETALA1 Gene Across Several Plant Species
To reveal the molecular mechanism ofAPETALA1 (AP1) gene and the evolution among different plants,we selected the complete nucleotide coding sequences ofAP1 gene from 8 different plant species for CUB analysis.Using R software,we performed a comparative analysis of codon bias and compositional dynamics of codon usage patterns in AP1 gene across eight different plant species by determining the GC contents,several genetic indices namely effective number of codons (ENC),relative synonymous codon usage(RSCU),and relative codon usage bias(RCBS)etc.Results showed codon usage in AP1 gene in plants were influenced by GC bias,mainly due to GC3s.The majority of optimal codons were A/U ending for the corresponding amino acid,of which ACA,AUA and CAG were over-represented codons in the AP1 gene of all the selected plant species.The codon usage pattern for AP1 in Paeonia lactiflora showed resemblance to that of Paeonia suffruticosa;similarly,and Prunus persica to Malus × domestica.Low Fop (Frequency of optimal codon) and high ENC values suggested a weaker codon bias observed for the AP1 gene in different plant species.
NETL
NSTL
万方数据
维普
