豆蔻属药用植物叶绿体基因组密码子偏性分析

目的明确豆蔻属药用植物叶绿体基因组蛋白编码基因密码子使用模式及影响因素。方法以草果Amomum tsao-ko、阳春砂Amomum villosum、白豆蔻Amomum kravanh和爪哇白豆蔻Amomum compactum叶绿体基因组50个共有蛋白编码基因为材料,利用CodonW 1.4.2软件、CUSP在线程序和Excel软件等分析基因密码子使用偏性参数和核苷酸组成。结果 4个豆蔻属物种叶绿体基因组具有相似的密码子使用模式,密码子第3位碱基GC含量为37.22%～37.31%,偏向使用NNA和NNT型密码子;4个物种的有效密码子数值(ENC)均在35以上,表明豆蔻属叶绿体基因组密码子偏性较弱。综合中性分析、有效密码子数(ENC-plot)分析、奇偶偏好性(PR2-plot)分析和对应性分析的结果显示豆蔻属叶绿体基因组密码子偏性主要受选择影响,同时突变等其它因素也对密码子的偏性产生一定的作用。在草果、阳春砂、白豆蔻和爪哇白豆蔻中分别确定了18、16、16、18个最优密码子,其中共有最优密码子13个。结论豆蔻属植物叶绿体基因组密码子第3位碱基偏向使用A/T结尾,密码子偏性受选择影响最大,同时还受到诸如突变等其它因素的影响。

Codon bias analysis of chloroplast genome in medicinal plants of Amomum Roxb.

Objective To determine the codon usage patterns and influencing factors of chloroplast genomic protein coding genes in medicinal plants of Amomum Roxb. Methods A total of 50 common protein coding genes of chloroplast genomes of Amomum tsao-ko, Amomum villosum, Amomum kravanh and Amomum compactum were used as materials, and the codon usage bias parameters and nucleotide composition were analyzed by CodonW 1.4.2 software, CUSP online program and Excel software. Results The chloroplast genomes of four Amomum species had similar codon usage patterns, and the GC content of third codon positions was 37.22-37.31%, which preferred to use NNA and NNT codons. The ENC values of the four species were all above 35, indicating that the codon bias of the chloroplast genome of Amomum is weak. The results of neutrality plot, ENC-plot, PR2-bias plot and correspondence analysis showed that the codon bias of Amomum chloroplast genome was mainly affected by selection, while other factors such as mutation also had a certain effect on codon bias. 18, 16, 16 and 18 optimal codons were identified in A. tsao-ko, A. villosum, A. kravanh and A. compactum, respectively, of which 13 were common optimal codons. Conclusion The third base of chloroplast genome of Amomum tends to use A/T ending,, and the codon bias is mostly affected by selection, as well as by other factors such as mutation.