掌叶覆盆子及其变种甜茶的质体基因组比较研究

Comparative analysis of plastomes of Rubus chingii and R.chingii var.suavissimus

掌叶覆盆子Rubus chingii和甜茶R.chingii var.suavissimus是优质的“药食同源”特色植物,经济效益显著,发展前景广阔。为探讨掌叶覆盆子及其变种甜茶的遗传结构及进化特征差异,该研究利用Illumina HiSeq XTen测序平台对2物种质体全基因组进行测序、组装、注释和特征分析,并采用生物信息学方法对其进行比较基因组分析和系统发育分析。结果表明,掌叶覆盆子和甜茶质体基因组呈现典型的环状四分体结构,由1个大单拷贝区(large single copy region,LSC)、1个小单拷贝区(small single copy region,LSC)和1对反向重复序列区(inverted repeat regions)组成。经比较分析,共鉴定出56个SSR位点,大部分由A和T组成。2个物种IR区边界基因结构保守,仅个别碱基差异。同时识别出3个高变区域:rps16⁃trnQ⁃psbK、trnR⁃at⁃pA和trnT⁃trnL,可作为潜在鉴定标记在未来进一步开发利用。基于最大似然法(maximum likelihood)与贝叶斯算法(Bayesian inference)所构建的系统发育分析结果显示,掌叶覆盆子和甜茶聚为一支,支持率达100%,两者最近缘物种为三花悬钩子R.trianthus。该研究从质体基因组层面上明确了两者间的遗传差异,以上结果将为后续的物种保护与开发利用奠定基础。

Rubus chingii and R.chingii var.suavissimus are unique dual⁃purpose plant resources,with significant nutraceutical,pharmaceutical,and economic value,as well as promising prospects for further development.To investigate the genetic structure and evolutionary characteristics of these two varieties,this study conducted plastome sequencing using the Illumina HiSeq XTen sequencing platform.Subsequently,the study performed assembly,annotation,and characterization of the genomes,followed by a comparative plastome and phylogenetic analysis using bioinformatics techniques.The results revealed that the plastomes of R.chingii and R.chingii var.suavissimus exhibited a tetrad structure,comprising a large single⁃copy region(LSC),a small single⁃copy region(SSC),and two inverted repeat regions(IRs).The study identified a total of 56 simple sequence repeats(SSRs)after comparative analysis,predominantly consisting of A and T.Furthermore,the structure of the IR boundary genes in both varieties was found to be highly conserved,with only minor nucleotide variations.Additionally,the study identified three highly variable regions:rps16⁃trnQ⁃psbK,trnR⁃atpA,and trnT⁃trnL,which held promise as potential identification marks for further development and utilization.Phylogenetic analysis results obtained by the maximum likelihood and Bayesian inference methods demonstrated a close clustering of R.chingii and R.chingii var.suavissimus(100%support),with their closest relatives being R.trianthus.This study,focusing on plastome⁃level genetic distinctions between these two varieties,lays a foundation for future species protection,development,and utilization.