Comparative analysis of flower-meristem-identity gene APETALA2 (AP2) codon in different plant species

作     者：WU Yan-qing LI Zhi-yuan ZHAO Da-qiu TAO Jun 

作者机构：College of Animal Science and Technology Yangzhou University Yangzhou 225009 P.R. China Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/College of Horticulture and Plant Protection Yangzhou University Yangzhou 225009 P.R. China 

出 版 物：《Journal of Integrative Agriculture》 (农业科学学报（英文版）)

年 卷 期：2018年第17卷第4期

页      面：867-877页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 090102[农学-作物遗传育种] 

基　　金：supported by the National Natural Science Foundation of China(31372097) the Agricultural Science&Technology Independent Innovation Fund of Jiangsu Province,China(CX(13)2014) 

主　　题：APETALA2(AP2) species codon usage bias(CUB) base composition dynamics 

摘      要：The flower-meristem-identity gene APETALA2(AP2), one of class-A genes, is involved in the establishment of the floral meristem and the forming of sepals and petals. Codon usage bias(CUB) identifies differences among species, meanwhile dynamic analysis of base composition can identify the molecular mechanisms and evolutionary relationships of a specific gene. In this study, eight coding sequences(CDS) of AP2 gene were selected from different plant species using the Gen Bank database. Their nucleotide composition(GC content), genetic index, relative synonymous codon usage(RSCU) and relative codon usage bias(RCUB) were calculated with R Software to compare codon bias and base composition dynamics of AP2 gene codon usage patterns in different plant species. The results showed that the usage of AP2 gene codons from different plant species were influened by GC bias, especially GC3 s. Overall, base composition analysis indicated that the usage frequency of codon AT in the gene coding sequence was higher than GC among AP2 gene CDS from different plant species. Furthermore, most AP2 gene CDSs ended with AT; AGA, GCU and UGU had relatively high RSCU values as the most dominant codon; the usage characteristic of the AP2 gene codon in Malus domestica was similar to that of Vitis vinifera; Paeonia lactiflora was similar to Paeonia suffruticosa and Solanum lycopersicum was similar to Petunia×hybrida. There was a moderate preference in the usage of AP2 gene codon among different plant species from relatively low frequency of optimal codon(Fop) values and high effective number of codons(ENC) value. This study has revealed the usage characteristics of the AP2 gene codon from the comparision of AP2 gene codon preference and base dynamics in different plant species and provide a platform for further study towards transgenic engineering and codon optimization.