摘要
为探讨兰科植物FT(FLOWERING LOCUS T)基因同义密码子使用偏好性,鉴定出该类基因的最优密码子,本研究以拟南芥FT基因为探针,从公共数据库(NCBI,Orchidbase,Orchidstra)筛选出24条兰科植物FT基因,并深入研究其密码子偏好性。结果表明,所有基因有效密码子数(effective number of codons,ENC)大于30,其中大于55的占41.7%,表明兰科植物FT基因的密码子偏好性较弱。中性绘图分析发现,密码子第3位GC含量(GC3)与前2位平均GC含量(GC12)的相关性较低,表明突变对密码子前两位和第三位碱基组成的影响不同,第三位密码子的偏性更多来自于自然选择。ENC与GC3的关联分析显示大部分基因的ENC值远低于预测值,小部分基因落在标准曲线附近,由此可见受到碱基突变影响,但很可能选择压力仍起主要作用。奇偶性分析发现,在目标基因密码子第三位上G/C和或者A/T不成比例分布,嘧啶含量要显著高于嘌呤含量,推测兰科植物FT基因密码子的使用模式除了碱基突变外,还受到其它因素的影响,例如自然选择压力等。鉴定出UUC等22个最优密码子,以G/C结尾的有20个,由此推断出基因偏好G/C结尾的密码子。
The study aimed to explore the codon usage bias of FLOWERING LOCUS T gene(FT) in Orchidaceae,and determine the optimal codons of the tested genes. The FT gene in Arabidopsis thaliana was served as the probe to query in NCBI, Orchidbase and Orchidstra, and 24 FT homologous genes of Orchidaceae were obtained. The parameter of codon usage bias was calculated by Codon W 1.4 and MEGA 5.1, and the causes that lead to codon bias was also be explored by neutrality analysis(GC12 vs. GC3), ENC-plots and parity rule 2 analysis. Finally,ΔRSCU methods was used to verify the optimal codons. The results showed that ENC value of all FT genes was higher 30, indicating the codon usage bias of tested genes was lower. There was a insignificant positive correlation(p>0.05) between GC12 and GC3 codons of FT genes, showing the effect of base mutationon GC12 was different from that on GC3, and natural mutation was the main factor in shaping codon usage. ENC-plot exhibited most tested genes fast below the ENC standard curve, while a small percentage of genes distributed near the standard curve. It was indicated natural mutation was the major influence on codon usage bias, rather than nucleotide composition. According to parity rule 2 analysis, G/C(or A/T) was not distributed proportionally on the 3rd position of codons, and the content of pyrimidine was significantly higher than purine. This result showed suggesting that had affected codon usage bias, also influenced by other factors independent of nucleotide composition, such as natural selection pressure. 22 optimal codons were identified, and 20 codons was ended in G/C in 3rdposition,which exhibited the tested genes had partia lity towards G/C. The study could lied the foundation of codon optimization in genetic engineering study of FT genes, which might be the breach on Early flowering breeding in Orchidaceae.
出处
《分子植物育种》
CAS
CSCD
北大核心
2016年第1期51-58,共8页
Molecular Plant Breeding
基金
国家自然科学基金(31360491)
中国博士后科学基金面上项目(133471)共同资助
