山矾属药用植物DNA条形码序列筛选研究——以GenBank数据为例
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摘要
目的:筛选出适合山矾属植物的DNA条形码序列。方法:基于GenBank数据库中下载的43种山矾属部分药用植物的核糖体基因片段和3个叶绿体基因片段,利用遗传距离法及分子系统学进行DNA条形码分析。结果:选取的4个序列片段中,变异位点及信息位点大小均为:ITS>psbA-trnH>matK>rbcL,但4个候选序列均没有明显的Barcoding Gap,其中ITS序列在种间的变异较大,而在种内的变异较小,较符合理想DNA条形码要求。通过对ITS序列进行聚类分析,其中邻接法鉴定成功率为83.87%,贝叶斯法鉴定成功率为80.65%。结论:本研究推荐ITS序列作为山矾属植物的DNA条形码候选序列,psbA-trnH作为补充序列。
引文
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[4] 张智,何桂娥,高洪勤,等.山矾属植物研究现状及其园林应用前景[J].中国农学通报,2012,28(22):308-311.
[5] Tamura K,Dudley J,Nei M,et al.MEGA4:molecular evolutionary genetics analysis(MEGA)software version 4.0[J]Molecular Biology and Evolution,2007,24(8):1596-1599.
[6] Ronquist F,Huelsenbeck JP.MrBayes 3:Bayesian phylogenetic inference under mixed models[J].Bioinformatics,2003,19(12):1572-1574.
[7] Darriba D,Taboada GL,Doallo R,et al.JModelTest 2:more models,new heuristics and parallel computing[J].Nature Methods,2012,9(8):772.
[8] Prosser SW,Dewaard JR,Miller SE,et al.DNA barcodes from century-old type specimens using next generation sequencing[J].Molecular Ecology Resources,2016,16(2):487-497.
[9] Braukmann TW,Kuzmina ML,Sills J,et al.Testing the efficacy of DNA barcodes for identifying the vascular plants of Canada.[J].PLoS One,2017,12(1):e0169515.
[10] 杨鹏,沈文华,石建明,等.唇形科常见药用植物DNA条形码的鉴定研究[J].中草药,2017,48(7):1397-1402.
[11] 杨慧洁,杨世海,张淑丽,等.药用植物DNA条形码研究进展[J].中草药,2014,45(18):2581-2587.
[12] Iftikhar R,Ashfaq M,Rasool A,et al.DNA barcode analysis of Thrips(Thysanoptera)diversity in Pakistan reveals cryptic species complexes[J].PLoS One,2016,11(1),e0146014.
[13] Xu S,Li D,Li J,et al.Evaluation of the DNA barcodes in Dendrobium(Orchidaceae)from mainland Asia[J].PLoS One,2015,10(1):e0115168.
[14] Yuan Q,Zhang B,Jiang D,et al.Identification of species and Materia Medica within Angelica L.(Umbelliferae)based on phylogeny inferred from DNA barcodes[J].Molecular Ecology Resources,2015,15(2):358-371.
[15] Wang DY,Wang Q,Wang YL,et al.Evaluation of DNA barcodes in Codonopsis(Campanulaceae)and in some large angiosperm plant genera[J].PLoS One,2017,12(2):e0170286.