紫麻属叶绿体全基因组特征及系统发育分析

Characterization of Complete Chloroplast Genome and Phylogenetic Analysis of Oreocnide

紫麻属(Oreocnide Miq.)为荨麻科(Urticaceae)常绿灌木或乔木,全株是良好的药用材料和制麻原料。开展紫麻属叶绿体基因组的相关研究对揭示紫麻属植物的遗传多样性和系统分类具有重要意义。本研究以NCBI数据库中已发布的10个紫麻属植物叶绿体全基因组序列为基础,对其进行基本特征比较和系统发育分析。结果显示,紫麻属叶绿体全基因组长度在156962~157464 bp之间,各物种注释基因数目均为129个,GC含量基本相同;在紫麻属叶绿体基因组中单核苷酸重复数量最多,占比96%,且以A/T碱基重复为主,其次是二核苷酸重复;紫麻属叶绿体全基因组序列具有较高的保守性,长梗紫麻和紫麻的ndhF基因和trnH基因与其他物种在IR/SC边界略有差异;经核苷酸多态性分析,筛选出了rpoB-trnC-GAC、clpP、rpl32-trnL-UAG、ccsD-ndhD和ycf1等5个高变区,主要位于基因间隔的非编码区。系统发育分析表明,长梗紫麻是紫麻属中较为原始的物种,三脉紫麻和宽叶紫麻的不同样本在下级各分支中存在嵌套现象。

Oreocnide is an evergreen shrub or tree of Urticaceae,the whole plant is used for medicinal and fibre materials.The study on the chloroplast genome of Oreocnide provides an important reference for revealing the genetic diversity and systematic classification of Oreocnide plants.Based on the whole genome sequences of the 10 Oreocnide species chloroplasts published in the NCBI database,the basic characteristics were compared and the phylogeny in the 10 chloroplast genomes.The results showed that the whole genome length of the Oreocnide chloroplast was from 156962 to 157464 bp,and the number of annotated genes were 129 genes with a close GC content among species.In the Oreocnide chloroplast genome,the number of single nucleotide repeats was the largest among all SSRs,accounting for 96%,mainly with a A/T base repeat,followed by dinucleotide repeats.The whole genome sequence of Oreocnide chloroplasts were genetically conservative.The ndhF gene and trnH gene in Oreocnide pedunculata and Oreocnide frutescens differ slightly from those in other species at the IR/SC border.Analysis of nucleotide polymorphism showed that five hypervariable regions were discovered in rpoB-trnC-GAC,clpP,rpl32-trnL-UAG,ccsD-ndhD and ycf1.These regions were mainly located in the non-coding region of gene spacing.Phylogenetic analysis showed that Oreocnide pedunculata was a relatively primitive species in the genus.Certain samples of Oreocnide trinervis and Oreocnide tonkinensis were nested with each other in the clades.