DNA宏条形码(metabarcoding)技术在中成药鉴定中的研究进展
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摘要
DNA宏条形码(metabarcoding)技术是一项传统DNA条形码与高通量测序技术相结合后衍生出的研究方法,该技术可快速、简便、有效地从多物种混合的生物样本中识别、还原其中的生物种类,目前在环境生物学研究中得到广泛运用。在市售中成药领域,掺伪、质量不稳定等因素严重制约了相关产业的可持续发展。该文介绍了DNA宏条形码技术的相关背景及其在中成药鉴定中的初步应用情况,同时还简述了研究过程中可能存在的问题并对DNA宏条形码技术发展进行了展望。
Metabarcoding technology is a research method derived from the combination of traditional DNA barcodes and highthroughput sequencing technologies. It can quickly,easily and efficiently identify and restore biological samples from multiple species.Biological species are currently widely used in environmental biology research. In the market of traditional Chinese medicines,adulteration and quality instability have severely restricted the sustainable development of the related industries. This article introduced the background of the metabarcoding technology and its preliminary application in the identification of Chinese patent medicines. It also outlined the possible problems in the research process and prospected to the development of the DNA metabarcoding technology.
Metabarcoding technology is a research method derived from the combination of traditional DNA barcodes and highthroughput sequencing technologies. It can quickly,easily and efficiently identify and restore biological samples from multiple species.Biological species are currently widely used in environmental biology research. In the market of traditional Chinese medicines,adulteration and quality instability have severely restricted the sustainable development of the related industries. This article introduced the background of the metabarcoding technology and its preliminary application in the identification of Chinese patent medicines. It also outlined the possible problems in the research process and prospected to the development of the DNA metabarcoding technology.
引文
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[8] Geml J,Gravendeel B,van der Gaag K J,et al. The contribution of DNA metabarcoding to fungal conservation:diversity assessment,habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands[J]. PLoS ONE,2014,9(6):e99852.
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[13]张映明.浅谈中成药临床合理应用[J].基层医学论坛,2013,16(8):1043.
[14]赵莹莹.我国中成药与美国植物药、日本汉方药在非处方药管理方面的比较研究[D].北京:北京中医药大学,2017.
[15]朱语眉,谢昊,王国华,等.非处方中成药在自我药疗中的风险与防范[J].中国药房,2014(23):2197.
[16]王璞,王聿成.非处方中成药不良反应发生原因的分析[J].云南中医学院学报,2013(2):47.
[17] Chen S P,Ng S W,Poon W T,et al. Aconite poisoning over 5yesrs:a case series in Hong Kong and lessons towards herbal safety[J].Drug Safety,2012,35(7):575.
[18] Mdicines:spurious/falsely-labelled/falsified/counterfeit(SFFC)medicines[EB/OL].[2018-06-05]. http://www. who. int/mediacentre/factsheets/fs275/en/. 2012.
[19]钱忠直,林瑞超,肖培根.中药鉴定与标准研究[J].中国中药杂志,2014,39(12):2153.
[20]高进,卢鹏,戴卉卿,等.中药现代制备工艺对不良反应的影响及相关对策[J].中国实验方剂学杂志,2014,20(14):52.
[21]崔占虎.中成药中原料药材的分子鉴别研究[D].包头:内蒙古科技大学,2014.
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[23]白虹,宁康,王长云.运用基于高通量测序和大数据挖掘的元基因组学方法分析中药制剂的物种成分[J].药学学报,2015,50(3):272.
[24] Coghlan M L,Haile J,Houston J,et al. Deep sequencing of plantand animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns[J].PLoS Genet,2012,8(4):436.
[25]田晓轩,刘杰,窦永杰,等.中成药大黄蛰虫丸的宏条形码基原鉴定[J].天津中医药,2014,31(4):234.
[26] Cheng X,Su X,Chen X,et al.Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing:the story for Liuwei Dihuang Wan[J]. Sci Rep,2014,4(1):5147.
[27] Coghlan M L,Garth Maker,Elly Crighton,et al. Combined DNA,toxicological and heavy metal analyses provides an auditing tool kit to improve pharmacovigilance of traditional Chinese medicine(TCM)[J]. Sci Rep,2015,5:17475.
[28]王丽丽.DNA条形码鉴定中药材和中药制剂的应用研究[D].北京:北京协和医学院,2016.
[29] Jia J,Xu Z,Song J Y,et al. Quality control of the traditional patent medicine Yimu Wan based on SMRT sequencing and DNA barcoding[J].Front Plant Sci,2017,8:926.
[30] Xin T Y,Xu Z,Jia J,et al. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule,real-time sequencing[J]. Acta Pharm Sin B,2018,8(3):488.
[31]石林春,刘金欣,宋经元,等.基于DNA metabarcoding技术的如意金黄散处方成分鉴定研究[J].中国科学:生命科学,2018,48(4):490.
[32] Hou D Y,Song J Y,Yao H,et al.Molecular identification of Corni Fructus and its adulterants by ITS/ITS2 sequences[J]. Chin J Nat Med,2013,11(2):121.
[33]段中岗,黄琼林,杨锦芬,等.适合中药材DNA条形码分析的DNA提取方法的研究[J].中药新药与临床药理,2009,20(5):480.
[34]程春松,谭天琪,龙泽,等.中药制剂DNA提取技术优化及其在人参类制剂分子鉴定中的应用[J].中草药,2015,46(17):2549.
[35] Sarkinen T,Staats M,Richardson J E,et al. How to open the treasure chest? Optimising DNA extraction from herbarium specimens[J].PLoS ONE,2012,7(8):e43808.
[36]马兰.DNA微型条形码和复合条形码研究进展[J].农业灾害研究,2013,3(6):58.
[37] Song M,Dong G Q,Zhang Y Q,et al. Identification of processed Chinese medicinal materials using DNA mini-barcoding[J].Chin J Nat Med,2017,15(7):481.
[38]王娟,侯艳芳,白准,等.广西莪术DNA条形码通用序列的筛选[J].中华中医药杂志,2015,30(1):100.
[39] Yang P,Zhou H,et al. Identification study of DNA barcode sequences in the medicinal plants of Polygonatum[J]. World Chin Med,2015,10(8):1173.
[40] Parducci L,Valiranta M,Salonen J S,et al. Proxy comparison in ancient peat sediments:pollen,macrofossil and plant DNA[J].Philos Trans R Soc Lond B Biol Sci,2015,370(1660):20130382.
[41] Chen S,Pang X,Song J,et al. A renaissance in herbal medicine identification:from morphology to DNA[J]. Biotechnol Adv,2014,32(7):1237.
[42]陈士林,郭宝林,张贵君,等.中药鉴定学新技术新方法研究进展[J].中国中药杂志,2012,37(8):1043.
[43] Zhou X,Li Y,Liu S,et al.Ultra-deep sequencing enables high-fidelityrecovery of biodiversity for bulk arthropodsamples without PCR amplification[J].Giga Sci,2013,2(1):4.
[44] Coissac E,Riaz T,Puillandre N. Bioinformatic challenges for DNA metabarcoding of plants and animals[J]. Mol Ecol,2012,21(8):1834.
[45] Pompanon F,Deagle B E,Symondson W O,et al. Who is eating what:diet assessment using next generation sequencing[J]. Mol Ecol,2012,21(8):1931.
[46]韦贵将,邹秉杰,陈之遥,等.新一代测序技术的研究进展[J].现代生物医学进展,2012,12(19):3789.
[47] Roberts R J,Carneiro M O,Schatz M C. The advantages of SMRT sequencing[J].Genome Biol,2013,14(7):405.
[48] Rees H C,Maddison B C,Middleditch D J,et al. The detection of aquatic animal species using environmental DNA--a review of e DNA as a survey tool in ecology[J].J Appl Ecol,2015,51(5):1450.
[2]李凤,李艳萍,张小蒙.宏基因组学的研究方法进展及应用概述[J].生物技术世界,2015(4):9.
[3]杨晓玲,施苏华,唐恬.新一代测序技术的发展及应用前景[J].生物技术通报,2010(10):76.
[4] Mardis E R. The impact of next-generation sequencing technologyon genetics[J].Trends Genet,2008,24(3):133.
[5] Taberlet P,Coissac E,Pompanon F,et al. Towards next-generation biodiversity assessment using DNA metabarcoding[J]. Mol Ecol,2012,21(8):2045.
[6]邢冉冉,吴亚君,陈颖.宏条形码技术在食品物种鉴定中的应用及展望[J].食品科学,2018,39(13):280.
[7] Prosser S W,Hebert P D. Rapid identification of the botanical and entomological sources of honey using DNA metabarcoding[J].Food Chem,2017,214:183.
[8] Geml J,Gravendeel B,van der Gaag K J,et al. The contribution of DNA metabarcoding to fungal conservation:diversity assessment,habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands[J]. PLoS ONE,2014,9(6):e99852.
[9] Zaiko A,Martinez J L,Schmidt-Petersen J,et al. Metabarcoding approach for the ballast water surveillance—An advantageous solution or an awkward challenge?[J]. Mar Pollut Bull,2015,92(1/2):25.
[10] Chown S L,Hodgins K,A. Biological invasions,climate change and genomics[J]. Evol Appl,2015,8(1):23.
[11] Khodakova A S,Smith R J,Burgoyne L,et al. Random whole metagenomic sequencing forforensic discrimination of soils[J]. PLoS ONE,2014,9(8):e104996.
[12]邱文琪,吴芊,宋明,等.宏基因组学与中医证候研究[J].中华中医药杂志,2017,32(9):4186.
[13]张映明.浅谈中成药临床合理应用[J].基层医学论坛,2013,16(8):1043.
[14]赵莹莹.我国中成药与美国植物药、日本汉方药在非处方药管理方面的比较研究[D].北京:北京中医药大学,2017.
[15]朱语眉,谢昊,王国华,等.非处方中成药在自我药疗中的风险与防范[J].中国药房,2014(23):2197.
[16]王璞,王聿成.非处方中成药不良反应发生原因的分析[J].云南中医学院学报,2013(2):47.
[17] Chen S P,Ng S W,Poon W T,et al. Aconite poisoning over 5yesrs:a case series in Hong Kong and lessons towards herbal safety[J].Drug Safety,2012,35(7):575.
[18] Mdicines:spurious/falsely-labelled/falsified/counterfeit(SFFC)medicines[EB/OL].[2018-06-05]. http://www. who. int/mediacentre/factsheets/fs275/en/. 2012.
[19]钱忠直,林瑞超,肖培根.中药鉴定与标准研究[J].中国中药杂志,2014,39(12):2153.
[20]高进,卢鹏,戴卉卿,等.中药现代制备工艺对不良反应的影响及相关对策[J].中国实验方剂学杂志,2014,20(14):52.
[21]崔占虎.中成药中原料药材的分子鉴别研究[D].包头:内蒙古科技大学,2014.
[22]中国药典.一部[S]. 2010:170.
[23]白虹,宁康,王长云.运用基于高通量测序和大数据挖掘的元基因组学方法分析中药制剂的物种成分[J].药学学报,2015,50(3):272.
[24] Coghlan M L,Haile J,Houston J,et al. Deep sequencing of plantand animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns[J].PLoS Genet,2012,8(4):436.
[25]田晓轩,刘杰,窦永杰,等.中成药大黄蛰虫丸的宏条形码基原鉴定[J].天津中医药,2014,31(4):234.
[26] Cheng X,Su X,Chen X,et al.Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing:the story for Liuwei Dihuang Wan[J]. Sci Rep,2014,4(1):5147.
[27] Coghlan M L,Garth Maker,Elly Crighton,et al. Combined DNA,toxicological and heavy metal analyses provides an auditing tool kit to improve pharmacovigilance of traditional Chinese medicine(TCM)[J]. Sci Rep,2015,5:17475.
[28]王丽丽.DNA条形码鉴定中药材和中药制剂的应用研究[D].北京:北京协和医学院,2016.
[29] Jia J,Xu Z,Song J Y,et al. Quality control of the traditional patent medicine Yimu Wan based on SMRT sequencing and DNA barcoding[J].Front Plant Sci,2017,8:926.
[30] Xin T Y,Xu Z,Jia J,et al. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule,real-time sequencing[J]. Acta Pharm Sin B,2018,8(3):488.
[31]石林春,刘金欣,宋经元,等.基于DNA metabarcoding技术的如意金黄散处方成分鉴定研究[J].中国科学:生命科学,2018,48(4):490.
[32] Hou D Y,Song J Y,Yao H,et al.Molecular identification of Corni Fructus and its adulterants by ITS/ITS2 sequences[J]. Chin J Nat Med,2013,11(2):121.
[33]段中岗,黄琼林,杨锦芬,等.适合中药材DNA条形码分析的DNA提取方法的研究[J].中药新药与临床药理,2009,20(5):480.
[34]程春松,谭天琪,龙泽,等.中药制剂DNA提取技术优化及其在人参类制剂分子鉴定中的应用[J].中草药,2015,46(17):2549.
[35] Sarkinen T,Staats M,Richardson J E,et al. How to open the treasure chest? Optimising DNA extraction from herbarium specimens[J].PLoS ONE,2012,7(8):e43808.
[36]马兰.DNA微型条形码和复合条形码研究进展[J].农业灾害研究,2013,3(6):58.
[37] Song M,Dong G Q,Zhang Y Q,et al. Identification of processed Chinese medicinal materials using DNA mini-barcoding[J].Chin J Nat Med,2017,15(7):481.
[38]王娟,侯艳芳,白准,等.广西莪术DNA条形码通用序列的筛选[J].中华中医药杂志,2015,30(1):100.
[39] Yang P,Zhou H,et al. Identification study of DNA barcode sequences in the medicinal plants of Polygonatum[J]. World Chin Med,2015,10(8):1173.
[40] Parducci L,Valiranta M,Salonen J S,et al. Proxy comparison in ancient peat sediments:pollen,macrofossil and plant DNA[J].Philos Trans R Soc Lond B Biol Sci,2015,370(1660):20130382.
[41] Chen S,Pang X,Song J,et al. A renaissance in herbal medicine identification:from morphology to DNA[J]. Biotechnol Adv,2014,32(7):1237.
[42]陈士林,郭宝林,张贵君,等.中药鉴定学新技术新方法研究进展[J].中国中药杂志,2012,37(8):1043.
[43] Zhou X,Li Y,Liu S,et al.Ultra-deep sequencing enables high-fidelityrecovery of biodiversity for bulk arthropodsamples without PCR amplification[J].Giga Sci,2013,2(1):4.
[44] Coissac E,Riaz T,Puillandre N. Bioinformatic challenges for DNA metabarcoding of plants and animals[J]. Mol Ecol,2012,21(8):1834.
[45] Pompanon F,Deagle B E,Symondson W O,et al. Who is eating what:diet assessment using next generation sequencing[J]. Mol Ecol,2012,21(8):1931.
[46]韦贵将,邹秉杰,陈之遥,等.新一代测序技术的研究进展[J].现代生物医学进展,2012,12(19):3789.
[47] Roberts R J,Carneiro M O,Schatz M C. The advantages of SMRT sequencing[J].Genome Biol,2013,14(7):405.
[48] Rees H C,Maddison B C,Middleditch D J,et al. The detection of aquatic animal species using environmental DNA--a review of e DNA as a survey tool in ecology[J].J Appl Ecol,2015,51(5):1450.