无籽刺梨及其近缘种叶绿体基因组序列比较分析

Comparative analyses on chloroplast genome sequence of Rosa sterilis and its related species

【目的】探讨无籽刺梨及其近缘种之间的系统发育关系,为蔷薇属植物后期分子鉴定和群体遗传研究奠定基础。【方法】从NCBI数据库下载了6种植物的叶绿体基因组序列,包括无籽刺梨和其近缘种。利用生物信息学方法对这些基因组序列进行了研究,包括基因组结构、重复序列、高变区序列以及基于叶绿体全基因组序列的系统发育关系。【结果】6种植物的叶绿体基因组呈环状四分体结构,其长度为156561~156749 bp,平均GC含量均为37.2%,且6种植物基因组的反向重复(inverted repeat,IR)区未表现出明显的扩张和收缩。在对蔷薇属植物叶绿体基因组序列进行比较分析时,筛选出了7个高变区序列,包括trnK-trnQ、psbM-trnY、ycf3-rps4、rps4-trnL、psbE-petG、rpl16 intron和ycf1。这些序列可作为候选标记,用于进一步研究蔷薇属植物的系统发育。同时,利用叶绿体全基因组序列重建了蔷薇属植物的系统发育树。结果表明,无籽刺梨和刺梨是独立的2个种类,其中无籽刺梨与贵州缫丝花有较近的亲缘关系,而刺梨与单瓣缫丝花有较近的亲缘关系。【结论】无籽刺梨及其近缘种之间叶绿体基因组结构高度相似,单拷贝区核苷酸多样性高于重复区。

【Objective】To explore the phylogenetic relationship between Rosa sterilis and its 5 related species,and to provide reference for molecular identification and genetic diversity.【Method】The chloroplast genome sequences from NCBI database were investigated on genomic structure,simple sequence repeat(SSR),hypervarieble regions,and phylogenetic relationship via systematic bioinformatics methods.【Result】These chloroplast genomes were 156561~156749 bp in length with an average GC content of 37.2%.They had a circular tetrad structure and had no obvious expansion or contraction in the inverted repeat region.Comparative analyses revealed 7 hypervariable regions including trnK-trnQ,psbM-trnY,ycf3-rps4,rps4-trnL,psbE-petG,rpl16 intron and ycf1,which potentially be provided as plastid markers for further work on phylogeny of Rosa.Phylogenetic tree revealed that R.sterilis and R.roxburghii were 2 segregated species.R.sterilis was closely related to R.kweichowensis,while R.roxburghii had a close relationship with R.roxburghii f.normali.【Conclusion】The chloroplast genome structure was highly similar between R.sterilis and its related species.The nucleotide polymorphism of the chloroplasts was higher in single copy region than inverted repeat regions.