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Article(id=1210148022114193806, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210148010437243088, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2022-0496, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1650902400000, receivedDateStr=2022-04-26, revisedDate=1652544000000, revisedDateStr=2022-05-15, acceptedDate=null, acceptedDateStr=null, onlineDate=1766451371935, onlineDateStr=2025-12-23, pubDate=1660233600000, pubDateStr=2022-08-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1766451371935, onlineIssueDateStr=2025-12-23, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1766451371935, creator=13701087609, updateTime=1766451371935, updator=13701087609, issue=Issue{id=1210148010437243088, tenantId=1146029695717560320, journalId=1189982191388893191, year='2022', volume='57', issue='8', pageStart='2245', pageEnd='2556', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1766451369151, creator=13701087609, updateTime=1766451533022, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1210148697808179705, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210148010437243088, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1210148697808179706, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1210148010437243088, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=2520, endPage=2527, ext={EN=ArticleExt(id=1210148022600733103, articleId=1210148022114193806, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=SNP double peak methods through chloroplast genome profiling for identifying Gentiana crassicaulis and two closely related species, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Gentiana crassicaulis Duthie ex Burk. is one of the plant sources of Gentianae Macrophyllae Radix (QinJiao). Gentiana tibetica King ex Hook. f. and Gentiana robusta King ex Hook. f. are relative species of G. crassicaulis. Due to the large intraspecific morphological variation, G. crassicaulis showed high morphological similarity with G. tibetica and G. robusta. And the distribution area of the three species overlaps to some extent, which makes it difficult to identify them. On the basis of morphological identification, the method of molecular identification of the three species was constructed in this study based on chloroplast genomes. The chloroplast genome of Gentiana tibetica is 148 765bp long, with LSC, SSC and IR 81 163 bp, 17 070 bp and 25 266 bp, respectively. The structure of the three is consistent. The chloroplast genome sequences of G. tibetica and G. crassicaulis are highly similar, and the number of variable sites is 9 (149 267 bp in total). Diagnostic SNP that could effectively identify the three species was screened and verified, and a dual-peak SNP detection method was established for the effective identification of each species and mixed samples. Our study provides basic data for the molecular identification of G. crassicaulis and its related species, and the arrangement of related Tibetan medicine.

, correspAuthors=Liang-hong NI, Zhi-li ZHAO, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2022 Acta Pharmaceutica Sinica. All rights reserved., copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Na-na GAO, Liang-hong NI, Zhi-li ZHAO, Dorje Gaawe), CN=ArticleExt(id=1210148025742267008, articleId=1210148022114193806, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=基于叶绿体全基因组序列的双峰法鉴定粗茎秦艽及其近缘物种, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为中药“秦艽”的基原植物之一, 而同为龙胆属秦艽组的西藏秦艽Gentiana tibetica King ex Hook. f.、粗壮秦艽Gentiana robusta King ex Hook. f.为其近缘的非国家药典品种。因存在较大的种内形态变异, 粗茎秦艽与西藏秦艽、粗壮秦艽间表现出较高的形态相似性, 且存在一定的同域分布, 为粗茎秦艽的鉴定带来了一定的难度。为有效鉴定中药秦艽国家药典品种粗茎秦艽与其近缘的非药典品种, 本文基于前期测定的粗茎秦艽、粗壮秦艽叶绿体基因组序列, 首次测定西藏秦艽叶绿体基因组序列, 筛选分子标记并构建这三个物种的分子鉴定方法。结果如下: ①获得西藏秦艽叶绿体基因组序列, 长度为148 765 bp, 大单拷贝区(LSC)、小单拷贝区(SSC) 分别为81 163 bp和17 070 bp, 反向重复区(IR) 为25 266 bp; ②粗茎秦艽、西藏秦艽、粗壮秦艽的叶绿体基因组结构一致; 粗茎秦艽与西藏秦艽的重复序列、SSR分布情况一致, 两个物种间叶绿体基因组变异位点数仅为9; ③筛选同时对这三个物种有效鉴定的单核苷酸多态性位点(SNP), 并验证稳定性; ④建立SNP双峰检测方法, 对各物种及混合样品进行有效鉴定。本工作可为粗茎秦艽及其近缘物种的DNA分子鉴定, 以及相关藏药品种的整理等工作提供基础资料。

, correspAuthors=倪梁红, 赵志礼, authorNote=null, correspAuthorsNote=
*倪梁红, Tel: 86-21-51322202, E-mail: ;
赵志礼, E-mail:
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Front Pharmacol, 2021, 12: 607200., articleTitle=The species identification in traditional herbal patent medicine, Wuhu San, based on shotgun metabarcoding, refAbstract=null)], funds=[Fund(id=1210148032667062389, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, awardId=82073959, language=CN, fundingSource=国家自然科学基金面上项目(82073959), fundOrder=null, country=null), Fund(id=1210148032771919994, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, awardId=81173654, language=CN, fundingSource=国家自然科学基金面上项目(81173654), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1210148026019091097, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, xref=null, ext=[AuthorCompanyExt(id=1210148026027479705, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, companyId=1210148026019091097, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1. 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Tibetan Traditional Medical College, Lhasa 850000, China), AuthorCompanyExt(id=1210148026165891752, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, companyId=1210148026144920229, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.西藏藏医药大学, 西藏 拉萨 850000)])], figs=[ArticleFig(id=1210148030104343493, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=SkphOCd7qgmfdFT/prtRUA==, figureFileBig=n37cSooq33duPgIN1XFrEw==, tableContent=null), ArticleFig(id=1210148030230172622, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 1, caption= Chloroplast genome map of <i>Gentiana tibetica</i>. Genes drawn inside of the map are transcribed in the clockwise direction and genes outside of the map are transcribed in the counter-clockwise direction. Genes belonging to different functional groups are expressed with different colors. Pseudogenes are marked with "<i>ψ</i>" and genes containing introns are marked with "*" , figureFileSmall=SkphOCd7qgmfdFT/prtRUA==, figureFileBig=n37cSooq33duPgIN1XFrEw==, tableContent=null), ArticleFig(id=1210148030498608100, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=lcnpDoDuHfRIIZT/TUa2oQ==, figureFileBig=MrAOqhaML2MT1lnn04W1pg==, tableContent=null), ArticleFig(id=1210148030586688492, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 2, caption= Repeat sequences in <i>G. tibetica, G. crassicaulis</i> and <i>G. robusta</i> chloroplast genomes. A: Frequency of the three repeat types by length; B: Repeat distribution among four different regions: IGS (intergenic spacer), CDS (coding sequence), CDS-IGS (part in CDS and part in IGS) and intron. F: Forward repeat sequence; P: Palindrome sequence; C: Complement repeat , figureFileSmall=lcnpDoDuHfRIIZT/TUa2oQ==, figureFileBig=MrAOqhaML2MT1lnn04W1pg==, tableContent=null), ArticleFig(id=1210148030678963191, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=g4KxK9PGPLOdjNRcaH/UEA==, figureFileBig=GIDxZZJRz2JeLyadtRYq2g==, tableContent=null), ArticleFig(id=1210148030792209408, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 3, caption= Simple sequence repeats in <i>G. tibetica, G. crassicaulis</i> and <i>G. robusta</i> chloroplast genomes. A: Frequency of different repeat types of SSRs; B: SSR distribution among four different regions: IGS (intergenic spacer), CDS (coding sequence), CDS-IGS (part in CDS and part in IGS) and intron , figureFileSmall=g4KxK9PGPLOdjNRcaH/UEA==, figureFileBig=GIDxZZJRz2JeLyadtRYq2g==, tableContent=null), ArticleFig(id=1210148030918037510, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=Ommr9T3uyjm22lACt7U7LA==, figureFileBig=IvB2mQYg6kBQXbNMVkfH+Q==, tableContent=null), ArticleFig(id=1210148031006117907, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 4, caption= Venn diagram of variable sites among cp genomes of <i>G. tibetica, G. crassicaulis</i> and <i>G. robusta</i> (the number represents the variation sites between the corresponding species) , figureFileSmall=Ommr9T3uyjm22lACt7U7LA==, figureFileBig=IvB2mQYg6kBQXbNMVkfH+Q==, tableContent=null), ArticleFig(id=1210148031282941981, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=WKaLJEhXuhwsqF7/vuvGsg==, figureFileBig=6FNqi3wx6SZib4VFsaSMog==, tableContent=null), ArticleFig(id=1210148031387799586, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 5, caption= The alignment of <i>ccs</i>A<i>-ndh</i>D of <i>G. crassicaulis, G. tibetica</i> and <i>G. robusta</i> , figureFileSmall=WKaLJEhXuhwsqF7/vuvGsg==, figureFileBig=6FNqi3wx6SZib4VFsaSMog==, tableContent=null), ArticleFig(id=1210148031522017324, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=xEicqyMEnEZy4yOmt+Bzfg==, figureFileBig=vPKzQ9eqDUHL5JGbJSuvcg==, tableContent=null), ArticleFig(id=1210148031673012280, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 6, caption= SNP peaks of <i>G. tibetica, G. crassicaulis</i> and <i>G. robusta</i> , figureFileSmall=xEicqyMEnEZy4yOmt+Bzfg==, figureFileBig=vPKzQ9eqDUHL5JGbJSuvcg==, tableContent=null), ArticleFig(id=1210148031790452799, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=UFNUdJpUwST5Xq9ddSa0Lw==, figureFileBig=T9w3hoxfISXMClBQr1LK2w==, tableContent=null), ArticleFig(id=1210148031891116100, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Figure 7, caption= SNP peaks of <i>G. tibetica</i> and <i>G. crassicaulis</i> with different proportions (<i>G. crassicaulis</i> : <i>G. tibetica</i>) , figureFileSmall=UFNUdJpUwST5Xq9ddSa0Lw==, figureFileBig=T9w3hoxfISXMClBQr1LK2w==, tableContent=null), ArticleFig(id=1210148031991779405, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesVoucher specimensNumberLocalityLongitude and latitude
G. crassicaulisQH2014053Banma, QinghaiN 32°46.608ʹ; E 100°49.695ʹ
GS2013012Maqu, GansuN 34°03.815ʹ; E 102°04.138ʹ
GS2016013Maqu, GansuN 34°03.815ʹ; E 102°04.138ʹ
GZ2016013Weining, GuizhouN 27°06.396ʹ; E 104°07.377
GZ2016022Weining, GuizhouN 27°06.393ʹ; E 104°07.362
SC2016013Kangding, SichuanN 29°54.618ʹ; E 101°59.538ʹ
SC2016022Daofu, SichuanN 30°29.862ʹ; E 101°29.727ʹ
YN2016013Lijiang, YunnanN 27°00.938ʹ; E 100°09.601ʹ
YN2016032Lijiang, YunnanN 27°25.266ʹ; E 100°25.518ʹ
2016XZ0083Basu, TibetN 30°07.148ʹ; E 97°16.886ʹ
2016XZ0092Basu, TibetN 30°08.997ʹ; E 97°17.618ʹ
2016XZ0112Changdu, TibetN 31°09.173ʹ; E 97°14.025ʹ
XZ2012143Dingqing, TibetN 31°21.458ʹ; E 95°52.533ʹ
2012XZ0143Dingqing, TibetN 31°21.458ʹ; E 95°52.533ʹ
G. tibetica2012XZ0043Linzhi, TibetN 29°09.303ʹ; E 94°12.861ʹ
2012XZ0062Linzhi, TibetN 29°37.450ʹ; E 94°21.184ʹ
2012XZ0073Linzhi, TibetN 29°46.809ʹ; E 94°24.584ʹ
XZ2013063Linzhi, TibetN 29°36.913ʹ; E 94°24.426ʹ
XZ2013073Linzhi, TibetN 29°09.303ʹ; E 94°12.861ʹ
XZ2013143Linzhi, TibetN 29°43.313ʹ; E 94°43.743ʹ
XZ2013163Linzhi, TibetN 29°35.739ʹ; E 94°20.763ʹ
2015XZ0023Longzi, TibetN 28°17.900ʹ; E 92°45.394ʹ
2015XZ0033Cuona, TibetN 27°52.891ʹ; E 91°47.500ʹ
2016XZ0043Yadong, TibetN 27°29.006ʹ; E 88°53.822ʹ
2016XZ0053Yadong, TibetN 27°31.745ʹ; E 88°58.493ʹ
2016XZ012-21Gongbujiangda, TibetN 30°00.689ʹ; E 92°59.311ʹ
G. robustaXZ2012013Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
XZ2012023Gongbujiangda, TibetN 29°52.151ʹ; E 92°34.714ʹ
XZ2012093Gongbujiangda, TibetN 29°52.160ʹ; E 92°40.557ʹ
XZ2012113Lhasa, TibetN 29°42.538ʹ; E 91°10.256ʹ
XZ2013013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2013183Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
XZ2014013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2014041Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2014051Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
2015XZ0053Cuona, TibetN 28°00.732ʹ; E 91°57.736ʹ
2016XZ0023Langkazi, Tibet, TibetN 29°02.849ʹ; E 90°23.746ʹ
J20140818013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
J20140819023Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
), ArticleFig(id=1210148032201494612, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Table 1, caption=

Sources of plant materials

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesVoucher specimensNumberLocalityLongitude and latitude
G. crassicaulisQH2014053Banma, QinghaiN 32°46.608ʹ; E 100°49.695ʹ
GS2013012Maqu, GansuN 34°03.815ʹ; E 102°04.138ʹ
GS2016013Maqu, GansuN 34°03.815ʹ; E 102°04.138ʹ
GZ2016013Weining, GuizhouN 27°06.396ʹ; E 104°07.377
GZ2016022Weining, GuizhouN 27°06.393ʹ; E 104°07.362
SC2016013Kangding, SichuanN 29°54.618ʹ; E 101°59.538ʹ
SC2016022Daofu, SichuanN 30°29.862ʹ; E 101°29.727ʹ
YN2016013Lijiang, YunnanN 27°00.938ʹ; E 100°09.601ʹ
YN2016032Lijiang, YunnanN 27°25.266ʹ; E 100°25.518ʹ
2016XZ0083Basu, TibetN 30°07.148ʹ; E 97°16.886ʹ
2016XZ0092Basu, TibetN 30°08.997ʹ; E 97°17.618ʹ
2016XZ0112Changdu, TibetN 31°09.173ʹ; E 97°14.025ʹ
XZ2012143Dingqing, TibetN 31°21.458ʹ; E 95°52.533ʹ
2012XZ0143Dingqing, TibetN 31°21.458ʹ; E 95°52.533ʹ
G. tibetica2012XZ0043Linzhi, TibetN 29°09.303ʹ; E 94°12.861ʹ
2012XZ0062Linzhi, TibetN 29°37.450ʹ; E 94°21.184ʹ
2012XZ0073Linzhi, TibetN 29°46.809ʹ; E 94°24.584ʹ
XZ2013063Linzhi, TibetN 29°36.913ʹ; E 94°24.426ʹ
XZ2013073Linzhi, TibetN 29°09.303ʹ; E 94°12.861ʹ
XZ2013143Linzhi, TibetN 29°43.313ʹ; E 94°43.743ʹ
XZ2013163Linzhi, TibetN 29°35.739ʹ; E 94°20.763ʹ
2015XZ0023Longzi, TibetN 28°17.900ʹ; E 92°45.394ʹ
2015XZ0033Cuona, TibetN 27°52.891ʹ; E 91°47.500ʹ
2016XZ0043Yadong, TibetN 27°29.006ʹ; E 88°53.822ʹ
2016XZ0053Yadong, TibetN 27°31.745ʹ; E 88°58.493ʹ
2016XZ012-21Gongbujiangda, TibetN 30°00.689ʹ; E 92°59.311ʹ
G. robustaXZ2012013Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
XZ2012023Gongbujiangda, TibetN 29°52.151ʹ; E 92°34.714ʹ
XZ2012093Gongbujiangda, TibetN 29°52.160ʹ; E 92°40.557ʹ
XZ2012113Lhasa, TibetN 29°42.538ʹ; E 91°10.256ʹ
XZ2013013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2013183Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
XZ2014013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2014041Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
XZ2014051Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
2015XZ0053Cuona, TibetN 28°00.732ʹ; E 91°57.736ʹ
2016XZ0023Langkazi, Tibet, TibetN 29°02.849ʹ; E 90°23.746ʹ
J20140818013Mozhugongka, TibetN 29°41.305ʹ; E 92°06.737ʹ
J20140819023Lhasa, TibetN 29°42.952ʹ; E 91°10.394ʹ
), ArticleFig(id=1210148032306352217, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
FeatureG. tibeticaG. crassicaulisG. robusta
GenBank IDKU975374KJ676538KT159969
Total length/bp148 765148 776148 911
GC content/%37.7137.7237.70
LSC length/bp81 16381 16481 164
SSC length/bp17 07017 07017 081
IR length/bp25 26625 27125 333
Total genes112112112
Duplicate genes in IR section181818
Genes encoding protein787878
rRNA genes444
tRNA genes303030
Pseudogenes222
), ArticleFig(id=1210148032398626911, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Table 2, caption=

Chloroplast genome features comparison results of G. tibetica, G. crassicaulis and G. robusta

, figureFileSmall=null, figureFileBig=null, tableContent=
FeatureG. tibeticaG. crassicaulisG. robusta
GenBank IDKU975374KJ676538KT159969
Total length/bp148 765148 776148 911
GC content/%37.7137.7237.70
LSC length/bp81 16381 16481 164
SSC length/bp17 07017 07017 081
IR length/bp25 26625 27125 333
Total genes112112112
Duplicate genes in IR section181818
Genes encoding protein787878
rRNA genes444
tRNA genes303030
Pseudogenes222
), ArticleFig(id=1210148032465735781, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
LSCSSCIRTotal
SNPInDelSNPInDelSNPInDelSNPInDel
A vs B52100163
C vs B2167396615932788
A vs C2117196615832285
A vs B vs C*00100010
), ArticleFig(id=1210148032558010475, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1210148022114193806, language=CN, label=Table 3, caption=

SNPs and InDels among cp genomes of G. tibetica, G. crassicaulis and G. robusta. A: G. crassicaulis; B: G. tibetica; C: G. Robusta.* Different with each other

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LSCSSCIRTotal
SNPInDelSNPInDelSNPInDelSNPInDel
A vs B52100163
C vs B2167396615932788
A vs C2117196615832285
A vs B vs C*00100010
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基于叶绿体全基因组序列的双峰法鉴定粗茎秦艽及其近缘物种
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高娜娜 1 , 倪梁红 1, * , 赵志礼 1, * , 嘎务 2
药学学报 | 研究论文 2022,57(8): 2520-2527
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药学学报 | 研究论文 2022, 57(8): 2520-2527
基于叶绿体全基因组序列的双峰法鉴定粗茎秦艽及其近缘物种
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高娜娜1, 倪梁红1, * , 赵志礼1, * , 嘎务2
作者信息
  • 1.上海中医药大学, 上海 201203
  • 2.西藏藏医药大学, 西藏 拉萨 850000

通讯作者:

*倪梁红, Tel: 86-21-51322202, E-mail: ;
赵志礼, E-mail:
SNP double peak methods through chloroplast genome profiling for identifying Gentiana crassicaulis and two closely related species
Na-na GAO1, Liang-hong NI1, * , Zhi-li ZHAO1, * , Dorje Gaawe2
Affiliations
  • 1. Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
  • 2. Tibetan Traditional Medical College, Lhasa 850000, China
出版时间: 2022-08-12 doi: 10.16438/j.0513-4870.2022-0496
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摘要
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粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为中药“秦艽”的基原植物之一, 而同为龙胆属秦艽组的西藏秦艽Gentiana tibetica King ex Hook. f.、粗壮秦艽Gentiana robusta King ex Hook. f.为其近缘的非国家药典品种。因存在较大的种内形态变异, 粗茎秦艽与西藏秦艽、粗壮秦艽间表现出较高的形态相似性, 且存在一定的同域分布, 为粗茎秦艽的鉴定带来了一定的难度。为有效鉴定中药秦艽国家药典品种粗茎秦艽与其近缘的非药典品种, 本文基于前期测定的粗茎秦艽、粗壮秦艽叶绿体基因组序列, 首次测定西藏秦艽叶绿体基因组序列, 筛选分子标记并构建这三个物种的分子鉴定方法。结果如下: ①获得西藏秦艽叶绿体基因组序列, 长度为148 765 bp, 大单拷贝区(LSC)、小单拷贝区(SSC) 分别为81 163 bp和17 070 bp, 反向重复区(IR) 为25 266 bp; ②粗茎秦艽、西藏秦艽、粗壮秦艽的叶绿体基因组结构一致; 粗茎秦艽与西藏秦艽的重复序列、SSR分布情况一致, 两个物种间叶绿体基因组变异位点数仅为9; ③筛选同时对这三个物种有效鉴定的单核苷酸多态性位点(SNP), 并验证稳定性; ④建立SNP双峰检测方法, 对各物种及混合样品进行有效鉴定。本工作可为粗茎秦艽及其近缘物种的DNA分子鉴定, 以及相关藏药品种的整理等工作提供基础资料。

粗茎秦艽  /  西藏秦艽  /  粗壮秦艽  /  叶绿体基因组  /  SNP标记  /  双峰检测法

Gentiana crassicaulis Duthie ex Burk. is one of the plant sources of Gentianae Macrophyllae Radix (QinJiao). Gentiana tibetica King ex Hook. f. and Gentiana robusta King ex Hook. f. are relative species of G. crassicaulis. Due to the large intraspecific morphological variation, G. crassicaulis showed high morphological similarity with G. tibetica and G. robusta. And the distribution area of the three species overlaps to some extent, which makes it difficult to identify them. On the basis of morphological identification, the method of molecular identification of the three species was constructed in this study based on chloroplast genomes. The chloroplast genome of Gentiana tibetica is 148 765bp long, with LSC, SSC and IR 81 163 bp, 17 070 bp and 25 266 bp, respectively. The structure of the three is consistent. The chloroplast genome sequences of G. tibetica and G. crassicaulis are highly similar, and the number of variable sites is 9 (149 267 bp in total). Diagnostic SNP that could effectively identify the three species was screened and verified, and a dual-peak SNP detection method was established for the effective identification of each species and mixed samples. Our study provides basic data for the molecular identification of G. crassicaulis and its related species, and the arrangement of related Tibetan medicine.

Gentiana tibetica  /  Gentiana crassicaulis  /  Gentiana robusta  /  chloroplast genome  /  SNP marker  /  double peak detection
高娜娜, 倪梁红, 赵志礼, 嘎务. 基于叶绿体全基因组序列的双峰法鉴定粗茎秦艽及其近缘物种. 药学学报, 2022 , 57 (8) : 2520 -2527 . DOI: 10.16438/j.0513-4870.2022-0496
Na-na GAO, Liang-hong NI, Zhi-li ZHAO, Dorje Gaawe. SNP double peak methods through chloroplast genome profiling for identifying Gentiana crassicaulis and two closely related species[J]. Acta Pharmaceutica Sinica, 2022 , 57 (8) : 2520 -2527 . DOI: 10.16438/j.0513-4870.2022-0496
正文
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粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为《中华人民共和国药典》 (2020年版) 收载的中药“秦艽”基原植物之一, 来源于龙胆科Gentianaceae龙胆属Gentiana秦艽组Section Cruciata, 根入药, 可祛风湿, 清湿热, 止痹痛, 退虚热[1, 2]。秦艽组植物在青藏高原呈现出丰富的物种多样性[3], 并由于杂交和多倍化等[4, 5], 秦艽组植物存在明显的种内形态变异, 以及近缘物种间表现出较高的形态相似性。在市场及应用中, 除了药典收载的秦艽4个基原品种外, 存在较多的混伪品。国内学者针对秦艽组植物及秦艽药材的鉴定开展了一系列的研究工作。罗焜等[6]应用ITS2条形码对秦艽药材及其多种混伪品进行鉴定研究; 熊波等[7]应用ITS和atpB-rbcL等多片段组合对西藏产4种秦艽组植物进行鉴定; 倪梁红等[8]应用ITS与叶绿体多片段组合构建甘肃产6种秦艽组植物的鉴定策略; 陆佳妮等[9]评价了线粒体nad1/b-c及nad5/d-e对秦艽组物种的鉴定意义; Liu等[10]测定了包括秦艽组8种在内的龙胆属6组30种植物的ITS及rbcL等序列, 构建的DNA条形码可用于秦艽4种基原植物的鉴定。但是, 因存在致同进化不完全, 秦艽组部分物种的ITS序列存在杂合, 需要结合克隆测序及基因分型; 同时因遗传背景相近, 常用条形码片段在部分近缘物种, 如粗茎秦艽与西藏秦艽, 麻花秦艽与粗壮秦艽等的鉴定中提供的信息位点有限。因此, 有待于寻找更为便捷、稳定的分子标记。本文以粗茎秦艽为切入点, 探讨秦艽药典品种与近缘的非药典品种的深入、高效的鉴定方法。
粗壮秦艽Gentiana robusta King ex Hook. f.、西藏秦艽Gentiana tibetica King ex Hook. f., 为与粗茎秦艽形态相近的非药典品种, 这三个物种间还存在一定的同域分布, 这些都为物种鉴定带来了一定的难度和复杂性。同时, 据文献[11]报道, 粗茎秦艽、西藏秦艽等均为藏药“解吉”的来源, 本课题组在西藏产解吉药材市场品调研中注意到, 因形态相近, 在解吉药材的采集、流通及应用中, 不同地区所涉及来源存在多样性, 影响相关藏药品种的进一步标准化研究。
前期, 本课题组在形态分类的基础上[12], 对粗茎秦艽、西藏秦艽和粗壮秦艽进行了植物形态学测量, 将大量形态学数据与数理统计方法结合, 细化各物种的繁殖器官(花及花序) 各部位的形态特征, 获得将这三个近缘物种有效区分的形态学参数, 为其形态鉴定提供了新思路[13]。但因秦艽的药用部位为根, 形态鉴定方法对其药材的鉴定具有局限性, 进一步构建相关物种的分子鉴定方法很有必要。
叶绿体普遍存在于绿色植物中, 拥有自身完整的一套基因组[14]。叶绿体基因组含有大量的遗传信息, 现已成为药用植物物种鉴定及系统进化研究的有力工具[15, 16]。相较于常用DNA条形码片段, 叶绿体基因组可提供更为丰富的信息位点, 同时, 被子植物的叶绿体DNA一般为母系遗传, 不存在多拷贝杂合现象[15], 便于序列分析。目前, 秦艽组多个物种已完成了叶绿体基因组测序[17-21]。基于叶绿体基因组序列可对长梗秦艽、全萼秦艽、达乌里秦艽、管花秦艽等物种进行有效分子鉴定[19, 20]; 同时, 基于叶绿体基因组序列的系统进化分析进一步阐明了龙胆属内秦艽组与多枝组的系统关系[21]。
本实验新完成西藏秦艽的叶绿体基因组测序, 结合前期已获得的粗茎秦艽、粗壮秦艽叶绿体基因组序列[18], 通过序列比较, 筛选出可同时对这三个物种进行有效鉴定的SNP位点。基于各物种分布区广泛采样的基础上, 进行SNP鉴别位点的稳定性验证。同时, 采用SNP双(多) 峰检测的方法[22], 对混合样品进行分析。本研究可为这粗茎秦艽及近缘物种的有效分子鉴定、遗传背景分析等工作提供依据。
材料与方法
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样品采集与鉴定  采集粗茎秦艽14个居群36个单株, 西藏秦艽12个居群33个单株, 粗壮秦艽13个居群35个单株(表 1), 样点覆盖各物种主要分布区。采集时将新鲜叶片用硅胶快速干燥, 得分子生物学实验材料, 备用。凭证标本经赵志礼教授鉴定, 保存于上海中医药大学药用植物标本室。
西藏秦艽叶绿体基因组测序  用改良的CTAB法[23]提取西藏秦艽(标本号: 2015XZ002-A) 的总DNA。参考本课题组方法[19], 获得西藏秦艽的叶绿体基因组序列, 进行叶绿体基因组的注释及结构分析。
叶绿体基因组比较  对粗茎秦艽、西藏秦艽、粗壮秦艽的叶绿体基因组的结构和DNA序列进行比较[19, 24]。分析物种间的变异位点及分布情况, 并筛选可同时对三个物种进行有效区分的SNP鉴别位点。
SNP鉴别位点验证  对SNP鉴别位点所在片段(ccsA-ndhD) 设计专属引物(上游引物: 5'-GACCCAA AAGAAACGTGGGC-3', 下游引物: 5'-CACTGTCGG TTGACAGGGTA-3'; 扩增产物长度: 450 bp)。对粗茎秦艽、西藏秦艽、粗壮秦艽所有样本进行PCR扩增, 程序为: 94 ℃, 5 min; 42× (94 ℃, 30 s; 59.9 ℃, 40 s; 72 ℃, 1 min); 72 ℃, 7 min。扩增产物经琼脂糖凝胶电泳检测后送上海生工公司应用Sanger法测序, 根据测序结果分析该位点在各物种内的稳定性。
SNP鉴别位点的混合样品检测  分别将三种秦艽的总DNA两两混合及三者混合, 对ccsA-ndhD片段进行扩增、测序, 观察测序峰图中SNP鉴别位点的峰形特征, 分析该位点对混合样品的鉴别能力。并分析样品的DNA混合比例与SNP峰图的相关性, 应用紫外分光光度法测定粗茎秦艽、西藏秦艽的总DNA浓度, 并配制成相同浓度; 然后分别选取两者比例为20∶1、10∶1、5∶1、1∶1、1∶5、1∶10、1∶20的总DNA混合溶液, 进行ccsA-ndhD片段的扩增及测序, 观察SNP峰的变化。
结果与分析
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1 西藏秦艽叶绿体基因组结构
西藏秦艽的叶绿体基因组总长148 765 bp, 呈环状, 共分为4个组成部分: 一个大单拷贝区(LSC, 81 163 bp), 一个小单拷贝区(SSC, 17 070 bp), 以及两个反向互补重复区(IRa, IRb, 各25 266 bp) (图 1)。共含有基因112个, 包括蛋白编码基因78个、tRNA基因30个、rRNA基因4个, 其中有18个基因在IR区重复。此外, 存在ψrps16和ψinfA两个假基因, rps16缺失第二外显子, infA序列中插入终止密码子。基因组的GC含量为37.71%, 其中IR区(43.37%) 高于LSC区(35.47%) 和SSC区(31.62%), 这与IR区的rRNA基因具有较高的GC含量(55.3%) 有关[25]。西藏秦艽叶绿体基因组的结构及基因组成与粗茎秦艽、粗壮秦艽一致[18], IR区的长度具有较明显差异(表 2)。
应用Reputer程序对西藏秦艽叶绿体基因组中的正向重复序列(F, forward repeat sequence)、反向重复序列(R, reverse repeat sequence)、正向互补序列(C, complement repeat) 和回文序列(P, palindrome sequence) 等4种重复序列进行分析。结果显示, 有32对重复序列, 包括15对F重复、16对P重复和1对C重复, 未检测到R重复。大部分的重复序列位于非编码区, 大概有1/4重复序列位于编码区, 分别位于ycf1、ycf2、psaA、psaB、trnG-UCC和trnG-GCC。另有2对重复序列跨编码区与基因间隔区排列。应用相同方法检测, 粗茎秦艽重复序列的分析结果与西藏秦艽完全一致; 粗壮秦艽重复序列的数目、分布情况与其他两个种存在较明显的差异(图 2)。
对西藏秦艽叶绿体基因组中的SSR进行分析, 结果显示, 共有41个SSR, 其中27个单核苷酸SSR、4个二核苷酸SSR、2个三核苷酸SSR、7个四核苷酸SSR和1个六核苷酸SSR。单核苷酸SSR占比例最大(65.9%), 并且均为A/T型, 这与文献[26]报道被子植物叶绿体基因组中SSR以A/T型占主导是相一致的。所有的二核苷酸SSR类型都是AT/TA。其中31个SSR (75.6%) 位于非编码区; 10个SSR位于编码基因, 包括rpoC2、rpoC1、atpB、ycf1和ndhF; 有1个单核苷酸SSR跨编码区与基因间隔区排列。应用相同方法检测, 粗茎秦艽与西藏秦艽的SSR类型及分布完全一致; 粗壮秦艽SSR的数目、分布情况与其他两个种存在较明显的差异(图 3)。
2 叶绿体基因组变异位点分析
将粗茎秦艽、西藏秦艽和粗壮秦艽的叶绿体基因组DNA序列进行全面比较分析。粗壮秦艽与西藏秦艽之间有415个变异位点, 包括327个单核苷酸多态性位点(SNP) 和88个插入缺失(InDel); 粗壮秦艽与粗茎秦艽之间有407个变异位点, 包括322个SNP和85个InDel; 西藏秦艽与粗茎秦艽序列相似度极高, 两者之间仅有9个变异位点, 包括6个SNP和3个InDel (图 4, 表 3)。
三个物种间同时存在差异的变异位点仅有1个, 为位于ccsA-ndhD片段的第159位点, 其中粗茎秦艽为G, 西藏秦艽为T, 粗壮秦艽为C (图 5)。该位点可作为同时区分这三个物种的潜在分子标记。
3 SNP鉴别位点验证
对粗茎秦艽36个单株、西藏秦艽33个单株、粗壮秦艽35个单株的ccsA-ndhD第159位点测序结果表明, 该位点在三个物种内部均高度稳定, 无种内变异。
结合GenBank已知叶绿体基因组序列, 对秦艽组10种植物的ccsA-ndhD该位点进行分析。结果表明, 西藏秦艽为T; 麻花艽、粗壮秦艽、大叶秦艽、达乌里秦艽、黄管秦艽、管花秦艽为C; 全萼秦艽、长梗秦艽和粗茎秦艽为G。该位点对西藏秦艽的鉴定有较好的专属性。
4 混合样品鉴定
分别将三种秦艽组物种的总DNA两两混合后进行ccsA-ndhD片段的扩增和测序。测序图谱中, 该SNP位点呈现相应两个碱基的重叠峰, 即粗壮秦艽和粗茎秦艽的混合样为C/G, 西藏秦艽和粗茎秦艽的混合样为T/G, 粗壮秦艽和西藏秦艽的混合样为C/T。将3个物种的总DNA混合后, 进行ccsA-ndhD片段的扩增和测序, 该SNP位点在测序峰图中呈现相应3个碱基的重叠峰(C/G/T)。结果表明, 该位点可有效区分这三个物种的混合样品(图 6)。
选取粗茎秦艽和西藏秦艽, 进一步探讨样品混合比例对检测结果的影响。结果表明, 混合比例与峰图中峰面积的比例呈现一定的相关性, 随着西藏秦艽在混合样品中的比例逐渐加大, 该位点处西藏秦艽位点T在峰图中的比例总体呈增大趋势(图 7)。但不同碱基的响应强度存在差异, 粗茎秦艽该位点处G的响应高于西藏秦艽T。当粗茎秦艽与西藏秦艽的比例为20∶1时, 测序峰图中仅可见粗茎秦艽的G位点, 而当粗茎秦艽与西藏秦艽的比例为1∶20时, 两个物种的位点G/T均非常明显; 当两者等比例时, 粗茎秦艽的G位点峰值明显高于西藏秦艽T。
讨论
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秦艽组物种间形态相近, 且存在种下变异幅度较大、同域分布的近缘种间存在自然杂交等现象[4, 5], 导致一些近缘物种的鉴定较难把握。粗茎秦艽为中药秦艽的来源之一, 西藏秦艽和粗壮秦艽, 为其形态相近的近缘物种, 为确保中药秦艽基原植物来源的准确性, 在植物形态测量鉴定方法基础上[13], 本研究基于粗茎秦艽、西藏秦艽和粗壮秦艽的叶绿体基因组序列, 筛选鉴别位点, 进一步建立相关近缘物种的分子鉴定方法。同时考虑到可能存在的种内基因型, 在各物种分布区广泛取样, 进行鉴别位点的稳定性验证, 筛选出ccsA-ndhD片段内可同时鉴定这三个物种的SNP位点。秦艽组10种植物的序列比较结果表明, 该位点对西藏秦艽的鉴定有较好的专属性。ccsA-ndhD为非常规的DNA条形码片段, 应用较少, 但在多个分类群的叶绿体基因组比较分析中, 均发现其具有较高的变异性[27, 28], 可结合相关分类群的遗传背景特征进一步开发相应的分子标记。
SNP在分子鉴定中有着广泛的应用, 尤其是对近缘物种的鉴定[29, 30]。本文进一步采用SNP双(多) 峰检测方法, 通过测序图谱的直接观察, 可方便、直观的对各物种及混合样品进行区分鉴定, 同时在一定范围内可反映混合比例。但该方法对多批次样品的检验效率较低, 同时在定量方面存在局限。随着高通量测序技术的发展, 应用宏条形码技术对混合药材、中成药的鉴定研究日益成熟[31-33], 可有效弥补以上缺陷。基于本实验结果, 下一步可开展粗茎秦艽及其近缘物种的宏条形码鉴定方法。
粗茎秦艽和西藏秦艽的叶绿体基因组序列高度相近, 仅有9处差异位点(9/149 267), 提示两者可能存在相近的母系来源。系统发育分析也表明, 西藏秦艽可能为一杂交物种, 其叶绿体基因组序列与粗茎秦艽相比未呈现出外类群特征, 而是处于粗茎秦艽种内变异范围, 且在系统树中两者完全聚为一支(另文发表)。两者在化学成分、药效活性等方面的差异, 也有待于进一步研究。同时藏药“解吉”的来源涉及秦艽组粗茎秦艽、西藏秦艽及粗壮秦艽等多种植物, 通过开展深入的系统性研究工作, 可为相关藏药材品种的鉴定、质量标准完善等工作提供科学依据。
作者贡献: 高娜娜是本文的第一作者, 负责分子生物学实验及稿件撰写; 嘎务负责民族植物学考察及样品采集工作; 倪梁红和赵志礼为本文的通讯作者, 负责样品分类学鉴定, 研究工作总体设计及稿件修改等工作。
利益冲突: 本文的研究内容无任何利益冲突。
基金
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  • 国家自然科学基金面上项目(82073959)
  • 国家自然科学基金面上项目(81173654)
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2022年第57卷第8期
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doi: 10.16438/j.0513-4870.2022-0496
  • 接收时间：2022-04-26
  • 首发时间：2025-12-23
  • 出版时间：2022-08-12
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  • 收稿日期：2022-04-26
  • 修回日期：2022-05-15
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国家自然科学基金面上项目(82073959)
国家自然科学基金面上项目(81173654)
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    1.上海中医药大学, 上海 201203
    2.西藏藏医药大学, 西藏 拉萨 850000

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*倪梁红, Tel: 86-21-51322202, E-mail: ;
赵志礼, E-mail:
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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