角蒿属药用植物叶绿体基因组比较及系统发育分析

Chloroplast genome comparison and phylogenetic analysis of five medicinal plants of Incarvillea

目的研究角蒿属Incarvillea Juss.药用植物叶绿体基因组特征、变异程度及系统发育关系,为角蒿属物种分子鉴定、系统发育及药用植物资源保护等研究提供参考。方法以5种角蒿属药用植物为研究对象,通过高通量测序获取密生波罗花叶绿体基因组,并结合同属4种药用植物的叶绿体基因组序列,利用生物信息学方法比较5种角蒿属药用植物叶绿体基因组之间的结构特征及变异程度,同时以凌霄为外类群分析了角蒿属的系统发育关系。结果5种角蒿属药用植物的叶绿体基因组为典型的四分体结构,均包含一个大单拷贝区、一个小单拷贝区及2个反向重复区。密生波罗花Incarvillea compacta的叶绿体基因组序列长度为150144 bp,GC含量为40%,共注释到基因119个,其中76个蛋白质编码基因、35个转运RNA(transfer RNA,tRNA)基因、8个核糖体RNA(ribosomal RNA,rRNA)基因。重复序列分析发现两头毛I.arguta叶绿体基因组重复序列数量最少,且只有两头毛同时含有4种类型的重复序列,其余4种药用植物的重复序列总数及重复类型相同。密生波罗花有44个简单重复序列(simple sequence repeats,SSRs),且以单核苷酸(A/T)重复为主。叶绿体基因组比较分析发现角蒿属内5种药用植物的叶绿体基因组中非编码区比基因编码区的变异程度大,黄波罗花I.lutea与其他4种药用植物相比,具有较高的序列变异,而两头毛在进化上最为保守,同时发现藏波罗花I.younghusbandii和密生波罗花的序列相似性较高;共线性结果表明,角蒿I.sinensis、密生波罗花及藏波罗花中存在程度不一的基因重排。选择压力分析结果表明在角蒿属5种药用植物中rps2、rps7、psbN蛋白编码基因均受到正选择。系统发育分析结果显示,密生波罗花与藏波罗花亲缘关系最近,与两头毛的亲缘关系最远。结论5种角蒿属植物在叶绿体基因组结构特征方面较为保守,但其变异程度存在差异。其中,两头毛的变异程度最低,进化上最保守。就亲缘关系而言,密生波罗花和藏波罗花的亲缘关系最近。基于叶绿体基因组构建的系统发育树在一定程度上可以揭示角蒿属物种的系统发育关系。

Objective To understand the chloroplast genome characteristics,degree of variation and phylogenetic relationship of medicinal plants of Incarvillea.This study will provide a reference for molecular identification,phylogeny and conservation resources of Incarvillea.Methods Chloroplast genomes of Incarvillea compacta were obtained by highthroughput sequencing,and combined with chloroplast genome sequences from four species of Incarvillea medicinal plants.Structural characteristics and variation degree of chloroplast genomes of five medicinal plants of Incarvillea were compared by bioinformatics method.And the phylogenetic relationship of Incarvillea was analyzed with Campsis grandiflora as an outgroup.Results The chloroplast genomes of five species of Incarvillea had a double stranded ring structure,including a long single copy region,a short single copy region and two reverse repeats.The chloroplast genome sequence length of I.compacta was 150,154 bp with a GC content of 40%.A total of 119 genes were annotated,including 76 protein-coding genes,35 tRNA genes,and eight rRNA genes.Sequence repeat analysis showed that only I.arguta contained four repeat types,and the repeat sequence number and repeat types of the other four medicinal plants were the same.There were 44 SSRs in I.compacta,and SSRs were mainly single nucleotide(A/T).Chloroplast genome comparative analysis found that the degree of variation the non-coding region of chloroplast genome revealed a greater degree than the gene coding region of five Incarvillea medicinal species.Compared to the other four medicinal species,I.lutea had higher sequence variation,but I.arguta is the most evolutionarily conservative.It was also found to have high sequence similarity between I.younghusbandii and I.compacta.Collinearity analysis showed that gene rearrangement was found to varying degrees in I.sinensis,I.compacta and I.younghusbandii.Results of selection pressure analysis showed that rps2,rps7 and psbN genes were positively selected in five medicinal plants of Incarvillea.Phylogenetic analysis revealed that I.compacta and I.younghusbandii were the closest in the genetic relationship,and the furthest relation between I.compacta and I.arguta.Conclusion The chloroplast genome structure of the five species of Incarvillea is conservative,but the degree of variation is different.Among them,I.arguta has the lowest degree of variation and is the most evolutionarily conservative.In terms of kinship,the relatives of I.compacta and I.younghusbandii are the closest.The chloroplast genome-based phylogenetic tree can reveal the phylogenetic relationship of Incarvillea species to a certain extent.