人参属植物叶绿体基因组特征及其进化的研究

Characteristics and Evolution of Panax Chloroplast Genomes

[目的]对人参属(Panax L.)物种叶绿体基因组特征及其系统发育进行研究,为我国人参属资源的遗传学研究和开发利用提供理论依据。[方法]基于14种人参属植物叶绿体基因组序列,利用生物信息学软件,对叶绿体基因组特征、序列重复、结构变异、基因进化和系统发育进行分析。[结果]人参属物种叶绿体基因组均为典型的四分体结构,包含114个unique基因。长重复序列主要为回文重复和正向重复,30~39 bp的重复序列最多,SSR大多为A/T重复,单核苷酸重复是最丰富的类型。人参属叶绿体基因组未发生基因重排,反向重复区(IR)与单拷贝区边界高度保守,鉴定的12个核苷酸高度可变热点中7个位于大单拷贝(LSC)区,5个位于小单拷贝(SSC)区。根据dN/dS比率,发现功能未知基因clpP、ycf1和ycf2受正选择作用。系统发育分析显示,屏边三七和三叶参位于基部支系,四倍体人参和西洋参与其他二倍体物种聚在不同支系,三七、竹节参和越南参则亲缘关系较近。[结论]人参属叶绿体基因组基因数目和顺序一致,基因组结构保守,重复序列数目和类型存在差异,单拷贝区核苷酸多态性高于IR区,正选择基因可能与物种的生态适应性有关。

Objective Characteristics and phylogeny of chloroplast genomes of the medicinally and economically valuable species in Panax genus were studied.Methods Using bioinformatics software,the properties,repeats,structural variation,evolution,and phylogeny of the genomes of chloroplasts from 14 ginseng species were analyzed.Results The genomes consisted of typical quadripartite structure with 114 unique genes.The long repeats in them were mainly of palindromic and forward types with a length between 30 bp and 39 bp.The simple sequence repeats were largely A/T type and most abundantly mononucleotides.No gene rearrangement occurred in the genomes was observed.The boundary between the inverted repeat region and the single copy region was highly conserved.Of the 12 regions with highly variable nucleotides,7 were in the large and 5 in the small single copy region.Indicated by the dN/dS ratios,the positive selection could occur on clpP,ycf1,and ycf2 with unknown functions.The phylogenetic analysis showed that P.stipulenatus and P.trifolius were in the basal lineage,the tetraploid P.ginseng and P.quinquefolius separated from other diploid species,while P.notoginseng,P.japonicus,and P.vietnamensis closely related.Conclusion The chloroplasts of the ginseng species examined were basically same in number and order of genomes,conservative in structure,but divert in number and type of repeats.The nucleotide polymorphism of the chloroplasts was higher in single copy region than inverted repeat regions.The positive selection genes identified in the study might result from the ecological adaptation of these Panax species.