忍冬属囊管组植物叶绿体基因组进化分析

Evolutionary analysis of chloroplast genomes of Sect.Isika(Lonicera)species

目的揭示忍冬属囊管组16种植物叶绿体基因组特征及系统发育关系。方法以16种囊管组植物为研究材料,利用CodonW、EMBOSS、Excel等软件分析其叶绿体基因组密码子使用偏好性;利用IRscope、mVISTA、DNAsp进行叶绿体基因组比较分析;利用PhyloSuite基于最大似然法及贝叶斯法2种方法构建系统发育树。结果结果显示ENC值为46.54~47.37,均大于35,密码子偏好性较弱。GCall含量范围为38.92%~39.22%,均小于40%,具有明显的A/U偏好性,且GC1>GC2>GC3,密码子第3位碱基以A/U为主。通过中性绘图、ENC-plot及PR2-plot分析,发现影响密码子使用偏好性的主要因素是自然选择。筛选出最优密码子7个,且密码子第3位均以A/U结尾。16种囊管组植物中均出现ycf1假基因。IR边界保守,差异较小。变异主要集中在非编码区,且单拷贝区域核苷酸多态性大于反向重复区域,存在更多的变异位点。系统发育分析结果显示,红花亚组与紫花亚组内物种系统发育位置与《中国植物志》存在差异。结论揭示了影响忍冬属囊管组植物密码子偏好性的因素。结合叶绿体基因组比较分析,系统发育分析,有助于进一步理解忍冬属植物的进化和适应机制。

Objective To explore the characteristic of chloroplast genomes and phylogenic relationship of 16 species of Sect.Isika(Lonicera).Methods The codon usage bias parameters of 16 Sect.Isika plants were analyzed by CodonW,EMBOSS,and Excel.Comparative analysis of chloroplast genome was performed using IRscope,mVISTA and DNAsp.And the phylogenetic tree was constructed by PhyloSuite using maximum likelihood method and Bayesian method.Results The results showed that the ENC values were 46.54—47.37,all of which were greater than 35,indicating a weak codon bias.The GCall content ranged from 38.92%to 39.22%,all values being less than 40%,which revealed a clear A/U bias as well as GC1>GC2>GC3 pattern,and the third position of codon tends to use A/U base.Through the analysis of neutrality plot,ENC-plot and PR2-plot,it was determined that natural selection was the primary factor influencing codon usage bias.Seven optimal codons of 16 Sect.Isika plants were screened out,and the third position of the codons all ended with A/U.The ycf1 pseudogenes were found in all 16 Sect.Isika plants.The IR boundaries were conserved,with little difference.The variable regions were mainly in the non-coding regions and the nucleotide polymorphism of the single-copy region was greater than that of the inverted repeat region,and there were more variable sites.The results of phylogenetic analyses showed that the phylogenetic positions of the species within the safflower subgroup and the purple flower subgroup differed from those of Flora Reipublicae Popularis Sinicae.Conclusion Factors affecting the codon bias of Sect.Isika(Lonicera)were revealed.By combining comparative chloroplast genome analysis and phylogenetic analysis,the study could enhance the understanding about evolutionary and adaptive mechanisms of this genus.