ITS2二级结构系统发育信息在茄属药用植物DNA条形码鉴定中的应用价值(1)
[摘要]ITS2是中药鉴定的核心DNA条形码之一，基于ITS2的中药鉴定方法已被纳入《中国药典》，但分辨力不足仍是制约其推广应用的主要因素，因此需要进一步挖掘其有助于中药鉴定的遗传信息。在细胞内，ITS2以二级结构形式发挥功能，这种结构所蕴含的丰富遗传信息是核酸序列所无法体现的。该研究以茄属Solanum 26个物种的40个样本为研究对象来探究ITS2二级结构在茄属药用植物鉴定中的价值。作者利用PicXAA-R，MASTR和LocARNA软件来比对二级结构，利用RNAstat软件将二级结构信息转为系统发育信息，最后利用最大简约法进行建树分析。研究结果表明将ITS2二级结构转化为系统发育信息后信息位点增加了88.57%，物种关系树上50%，75%，90%以上支持率的支系分别增加了19.05%，66.67%，66.67%，从而很好地解决了茄属几种药用植物的鉴定问题。鉴于以上结果，作者建议将ITS2二级结构信息作为系统发育信息的有益补充加入到目前DNA条形码分析中。
[关键词]DNA条形码； ITS2二级结构； 药用植物； 茄属
, 百拇医药
[Abstract]Internal transcript spacer 2 (ITS2) is one of the broadly used standard core barcodes and also the only nuclear barcode in identification of Chinese traditional medicine. Although the DNA barcode method based on ITS2 is popular and has been used in Chinese Pharmacopoeia， its low discriminatory efficiency is still a problem to its extensive application. Therefore， further study is still necessary to explore its phylogenetic information for medicinal plants identification. In cells， ITS2 activity is based on its secondary structure. The secondary structures are particularly useful in phylogenetic analysis because they include information not found in the primary sequence. In this study ITS2 secondary structure of 40 samples from 26 species were predicted and used to explore their utility in addressing the identification problems of Chinese traditional medicine in Solanum. The secondary structures were predicted and aligned， and their consensus models were generated using the three different software of LocARNA， MASTR and PicXAA-R. RNAstat software was used to transform the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the phylogenetic information increased 88.57% after ITS2 secondary structure information has been added， and then the support values above 50%， 75% and 90% in the tree increased 19.05%， 66.67% and 66.67%， respectively， indicating that the identification of Solanum medical plants has been well resolved. Thus， our analysis suggests that ITS2 secondary structure information should be incorporated into the current DNA barcoding analysis as a beneficial supplement of phylogenetic information.
, 百拇医药
[Key words]DNA barcode； ITS2 secondary structure； medical plants； Solanum
DNA條形码技术作为一种新兴的分子鉴定技术，近年来受到广泛的关注。该技术是利用一种短而标准的DNA片段对物种进行快速而准确鉴定的方法[1-2]。由于它不受物种的形态学特征及发育阶段的限制，且准确性较高，在药用植物鉴定中备受关注。ITS(internal transcribed spacer)具有进化速率快、易于扩增、通用性好和双亲遗传等优点，已成为植物系统发育与进化研究中最重要的分子标记之一[3-5]。ITS2是ITS系统发育信息的主要来源，它在物种水平甚至种下水平都具有明显的序列变异，具有更高的系统发育学价值，因此被建议作为种子植物、真菌物种鉴定的DNA条形码[6-8]。在药用植物鉴定中基于ITS2的药用植物鉴定方法已被《中国药典》收录[9]。尽管ITS2作为DNA条形码有诸多优点，然而它还不能像COI在动物中那样成为物种鉴定的理想DNA条形码，主要原因是分辨力依然较低[10]。提高分辨率的传统做法是增加单一DNA片段的长度或片段组合数，然而这种方法费时费力，更重要的是随着基因片段的增加，PCR成功率呈几何倍数下降[11-12]，不适用于像中药材这样DNA容易降解的材料。因此，如何在不增加片段长度的情况下提高DNA条形码的分辨率是解决问题的关键。, http://www.100md.com(杨烁 薛渊元 李美慧 赵奉熙 赵宏 张伟)
[关键词]DNA条形码； ITS2二级结构； 药用植物； 茄属
, 百拇医药
[Abstract]Internal transcript spacer 2 (ITS2) is one of the broadly used standard core barcodes and also the only nuclear barcode in identification of Chinese traditional medicine. Although the DNA barcode method based on ITS2 is popular and has been used in Chinese Pharmacopoeia， its low discriminatory efficiency is still a problem to its extensive application. Therefore， further study is still necessary to explore its phylogenetic information for medicinal plants identification. In cells， ITS2 activity is based on its secondary structure. The secondary structures are particularly useful in phylogenetic analysis because they include information not found in the primary sequence. In this study ITS2 secondary structure of 40 samples from 26 species were predicted and used to explore their utility in addressing the identification problems of Chinese traditional medicine in Solanum. The secondary structures were predicted and aligned， and their consensus models were generated using the three different software of LocARNA， MASTR and PicXAA-R. RNAstat software was used to transform the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the phylogenetic information increased 88.57% after ITS2 secondary structure information has been added， and then the support values above 50%， 75% and 90% in the tree increased 19.05%， 66.67% and 66.67%， respectively， indicating that the identification of Solanum medical plants has been well resolved. Thus， our analysis suggests that ITS2 secondary structure information should be incorporated into the current DNA barcoding analysis as a beneficial supplement of phylogenetic information.
, 百拇医药
[Key words]DNA barcode； ITS2 secondary structure； medical plants； Solanum
DNA條形码技术作为一种新兴的分子鉴定技术，近年来受到广泛的关注。该技术是利用一种短而标准的DNA片段对物种进行快速而准确鉴定的方法[1-2]。由于它不受物种的形态学特征及发育阶段的限制，且准确性较高，在药用植物鉴定中备受关注。ITS(internal transcribed spacer)具有进化速率快、易于扩增、通用性好和双亲遗传等优点，已成为植物系统发育与进化研究中最重要的分子标记之一[3-5]。ITS2是ITS系统发育信息的主要来源，它在物种水平甚至种下水平都具有明显的序列变异，具有更高的系统发育学价值，因此被建议作为种子植物、真菌物种鉴定的DNA条形码[6-8]。在药用植物鉴定中基于ITS2的药用植物鉴定方法已被《中国药典》收录[9]。尽管ITS2作为DNA条形码有诸多优点，然而它还不能像COI在动物中那样成为物种鉴定的理想DNA条形码，主要原因是分辨力依然较低[10]。提高分辨率的传统做法是增加单一DNA片段的长度或片段组合数，然而这种方法费时费力，更重要的是随着基因片段的增加，PCR成功率呈几何倍数下降[11-12]，不适用于像中药材这样DNA容易降解的材料。因此，如何在不增加片段长度的情况下提高DNA条形码的分辨率是解决问题的关键。, http://www.100md.com(杨烁 薛渊元 李美慧 赵奉熙 赵宏 张伟)