吴茱萸属4种药用植物的叶绿体基因组比较与系统发育分析

Chloroplast Genome Comparison and Phylogenetic Analysis of Four Medicinal Plants of Evodia

目的:明确楝叶吴萸、臭辣吴萸、吴茱萸和石虎4种药用植物叶绿体基因组特征与系统发育关系,为吴茱萸药材的分子鉴定提供依据。方法:使用CTAB法提取叶片总基因组DNA,通过Illumina NovaSeq 6000平台测序,再用SPAdes软件组装叶绿体基因组序列,利用condonW、REPuter、mVISTA等软件进行序列特征分析并构建ML系统发育树。结果:4种吴茱萸属植物叶绿体基因组为典型的四分体结构,基因组大小在158563~158762 bp之间,总GC含量为38.34%~38.37%。均注释到134个编码基因,包括89个蛋白编码基因(PCGs),37个tRNA基因和8个rRNA基因。共检测到79~98个简单重复序列(SSR)和35~41个长重复序列。叶绿体基因组比较分析表明4个物种的反向重复区(IR)边界存在差异,单拷贝区(SC)比IR区表现出更高的变异性,筛选出了trnS-trnG、ycf4-cemA和psbM-trnA等10个高多样性片段,这些片段可用于吴茱萸属物种鉴定和系统发育研究。系统发育分析结果表明,吴茱萸与石虎聚为一支,楝叶吴萸和臭辣吴萸聚为一支,且这两支互为姊妹关系。结论:本研究为芸香科植物的分类、系统发育和分子育种等研究提供了有价值的遗传信息。

Objective:To clarify the chloroplast(CP)genome characteristics and phylogenetic relationships of four medicinal plants,Lianyezhuyu(Tetradium glabrifolium),Choulazhuyu(Evodia fargesii Dode),Wuzhuyu(Euodia rutaecarpa)and Shihu(Euodia rutaecarpa var.officinalis),so as to provide a basis for molecular identification of Evodia medicinal materials.Methods:The total genomic DNA of leaves was extracted using CTAB method,sequenced by Illumina NovaSeq 6000 platform,then the chloroplast genome sequences were assembled by SPAdes software.CondonW,REPuter,mVISTA and other software was used to sequence features analysis and construction of ML phylogenetic tree.Results:The CP genomes of four species of Euodia were typical tetrad structure,the genome size was between 158563 to 158762 bp,and the total GC-content was 38.34%-38.37%.134 coding genes were annotated,including 89 protein coding genes(PCGs),37 tRNA genes,and 8 rRNA genes.A total of 79-98 simple repeat sequences(SSR)and 35-41 long repeat sequences were detected.Comparative analysis of CP genomes showed that the reverse repeat region(IR)boundaries differed among the four species,and the single copy region(SC)showed higher variability than the IR region.10 highly diverse fragments,such as trnS-trnG,ycf4-cemA,and psbM trnA,were screened,which could be used for species identification and phylogenetic research of Evodia.Phylogenetic analysis showed that Wuzhuyu(Euodia rutaecarpa)and Shihu(Euodia rutaecarpa var.officinalis)were clustered into one branch,Lianyezhuyu(Tetradium glabrifolium)and Choulazhuyu(Evodia fargesii Dode)were clustered into another single branch,and the two branches were sister to each other.Conclusion:This study provides valuable genetic information for the classification,phylogeny and molecular breeding of Rutaceae plants.