10种植物PSY基因密码子使用偏好性分析

选取10种植物PSY基因的CDS编码区序列,通过计算序列的碱基组成、有效密码子数(ENC)、同义密码子相对使用度(RSCU)等相关参数,并对这些序列进行ENC绘图与奇偶性分析,揭示10种植物对PSY基因密码子的使用偏好性。结果表明10种植物对于PSY基因密码子使用优先选择含有A和U末端密码子。ENC图显示除突变影响PSY基因密码子使用偏好性以外,还存在其他因素的影响。通过对RSCU值聚类分析发现,10种植物中含有UUG、AGA、AGG、GGA、GAU、ACA、GUU、CCU、GCU、UCU、UCA的密码子为最优密码子(RSCU值1.6)。DANMAN结果显示GAAGATGC是10种植物所含有的最长的保守区域。以辣椒PSY基因为例,预测得到大肠杆菌和酿酒酵母是最合适的辣椒PSY基因的宿主。

Codon Usage Bias Analysis for Octahydrolycopene Synthase Gene(PSY) from Ten Plant Species

The CDS coding region of the ten plant PSY gene was selected in this study, and the base composition, effective number of codon, and other related parameters were calculated,the factors in codon usage were presumed busing ENC-plot and PR2 plot(parity analysis). The results showed that ten plants preferentially chose A and U-terminal codons for PSY codon usage. The ENC-plot showed that in addition to the use of the PSY codon caused by the mutation, there were additional factors. Cluster analysis of RSCU values revealed that UUG,AGA,AGG,GGA,GAU,ACA,GUU,CCU,GCU,UCU and UCA were the optimal codons in ten plants (RSCU value>1.6). The DANMAN results showed that GAAGATGC was the longest conserved region set out in 10 plants. In addition, we took pepper PSY as an example, it was predicted that E.coli and S.cerevisiae were the most suitable hosts for the PSY gene.