肉苁蓉属植物叶绿体基因组密码子偏好性分析

Codon use bias analysis of chloroplast genome of Cistanche

目的明确肉苁蓉属药用植物叶绿体基因组密码子使用偏性及影响因素。方法以肉苁蓉Cistanche deserticola、盐生肉苁蓉C.salsa、沙苁蓉C.sinensis和管花肉苁蓉C.tubulosa为研究材料,利用CUSP在线软件、CodonW 1.4.2、SPSS、Microsoft Excel等软件分析其基因密码子使用偏性参数。结果4个肉苁蓉属植物叶绿体基因组的密码子使用模式相似,密码子均以第3位碱基A/T结尾且密码子使用更偏向A/T碱基;4个物种的有效密码子数值(effective number of codon,ENC)均大于35,说明肉苁蓉属物种叶绿体基因密码子偏好性较弱。中性绘图分析、有效密码字数(ENC-plot)分析、奇偶偏好性(PR2-plot)分析和对应性分析的结果均说明自然选择是影响肉苁蓉属叶绿体基因组密码子偏好性的主要因素。利用同义密码子的相对使用频率(relative synonymous codon usage,RSCU)值筛选出肉苁蓉属4个物种共同拥有4个最优密码子。结论对肉苁蓉属4个物种叶绿体基因组密码子使用偏性进行分析,揭示了影响其密码子偏好性的影响因素,为进一步探讨肉苁蓉属植物的系统进化、环境适应性和品种改良提供了理论基础。

Objective To clarify the codon usage bias and influencing factors of chloroplast genome in four medicinal plants of Cistanche spp.Methods The codon usage bias parameters of Cistanche deserticola,C.salsa,C.sinensis and C.tubulosa were analyzed by CUSP,CodonW 1.4.2,SPSS and Microsoft Excel.Results The chloroplast genomes of four Cistanche species had similar codon usage patterns,with the third base of the codons all ending in A/T and tending to use the A/T bases more favorably.The ENC(effective number of codon)values of the four species were all above 35,indicating that the codon preference of the chloroplast genes in Cistanche spp.is weak.The results of neutrality plot,ENC-plot,PR2-bias plot and correspondence analysis indicated that natural selection was the main factor influencing chloroplast genome codon usage bias in Cistanche spp.The RSCU(relative synonymous codon usage)values were used to identify four optimal codons shared by four species of Cistanche spp.Conclusion In this study,we analyzed the codon usage bias of chloroplast genomes of four species of Cistanche spp.and revealed the influencing factors affecting codon bias,which provided the corresponding theoretical basis for studying the systematic evolution,environmental adaptation and breed improvement of Cistanche spp.at molecular level.