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Article(id=1308841190074704441, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308840985296204417, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2025-1377, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1763481600000, receivedDateStr=2025-11-19, revisedDate=1768147200000, revisedDateStr=2026-01-12, acceptedDate=null, acceptedDateStr=null, onlineDate=1789981656807, onlineDateStr=2026-09-21, pubDate=1778515200000, pubDateStr=2026-05-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1789981656807, onlineIssueDateStr=2026-09-21, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1789981656806, creator=13701087609, updateTime=1789981656806, updator=13701087609, issue=Issue{id=1308840985296204417, tenantId=1146029695717560320, journalId=1189982191388893191, year='2026', volume='61', issue='5', pageStart='1435', pageEnd='1880', issueExtLink='null', onlineDate='null', pubDate='1778515200000', pubDateStr='2026-05-12', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1789981607984, creator='13701087609', updateTime=1789984207975, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1308851890515968861, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308840985296204417, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1308851890515968862, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308840985296204417, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=1841, endPage=1851, ext={EN=ArticleExt(id=1308841190288613946, articleId=1308841190074704441, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Analysis of whole-GEnome for medicinal species identification of Citrus, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Citrus plants are economically and medicinally important crops worldwide. However, due to the highly complex genetic background of the genus, the accurate identification of medicinal species within this genus remains a major challenge. In this study, we employed the analysis of whole-GEnome (AGE), also known as the Shizhen Method, to conduct bioinformatics analysis on 49 genomes from 15 Citrus species, successfully constructing a candidate species-specific target sequence library that covers these species. The number of specific target sequences per species predominantly ranges from 10 000 to 100 000. From this candidate library, species-specific target sequences were selected for the corresponding species. Their high specificity was subsequently verified using Sanger sequencing and CRISPR-Cas12a technology, which confirmed their efficacy in identifying medicinal Citrus species. Based on this foundation, we established an AGE-based identification system for closely related Citrus species, which enabled the precise authentication of 30 commercial samples of Citri Reticulatae Semen and its decoction pieces. This study demonstrates that the AGE can be used for the accurate identification of medicinal Citrus species, which breaks through the bottlenecks of traditional methods and effectively resolves the identification challenges. It thereby provides technical support for quality control of Chinese herbal medicine and clinical medication safety.

, authors=Na-na ZHANG1, Yu-tong GAN1, Tian-yi XIN1, Zhi-jie SHI1, Wen-jie XU1, Jing-yuan SONG1, 2, *, authorsList=Na-na ZHANG, Yu-tong GAN, Tian-yi XIN, Zhi-jie SHI, Wen-jie XU, Jing-yuan SONG, authorCompany=null, correspAuthors=Jing-yuan SONG, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2026 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, fund=null), CN=ArticleExt(id=1308841193295929925, articleId=1308841190074704441, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=基于时珍法的柑橘属药用物种鉴定研究, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

柑橘属植物是世界上广泛种植的经济作物, 具有显著的药用价值和经济价值。然而, 由于柑橘属遗传背景高度复杂, 该属药用物种的准确鉴定面临挑战。本研究基于全基因组分析法(analysis of whole-GEnome, AGE), 又称为时珍法, 对柑橘属15个物种的49个基因组进行生物信息学分析, 成功构建涵盖15个物种的候选特异靶标序列库, 各物种靶标序列数量主要集中在10 000~100 000条之间。从候选特异靶标序列库中为相应物种选取特异靶标序列, 并通过Sanger测序和CRISPR-Cas12a技术证实选取的特异靶标序列具有高度特异性, 可有效鉴定柑橘属药用物种。在此基础上构建基于时珍法的柑橘属近缘物种鉴定体系, 实现30份市售橘核药材及饮片的准确鉴定。本研究证明时珍法可用于柑橘属药用物种的准确鉴定, 突破传统鉴定方法的瓶颈, 有效解决柑橘属药用物种的鉴定难题, 为中药材质量控制和临床用药安全提供技术支撑。

, authors=张娜娜1, 甘雨桐1, 辛天怡1, 史志杰1, 许文杰1, 宋经元1, 2, *, authorsList=张娜娜, 甘雨桐, 辛天怡, 史志杰, 许文杰, 宋经元, authorCompany=null, correspAuthors=宋经元, authorNote=

作者贡献:

张娜娜负责实验设计、样本收集、实验工作、数据分析、文章撰写及修改; 甘雨桐负责数据管理及分析, 参与实验工作和稿件修改; 辛天怡负责稿件修改; 史志杰参与实验工作和稿件修改; 许文杰参与稿件修改; 宋经元负责实验设计、总体把关和稿件修改等工作。

, correspAuthorsNote=
宋经元, Tel: 86-10-57833199, E-mail:
, copyrightStatement=版权所有©《药学学报》编辑部2026, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=H6+jbUT/+TIAEgC67Fl6GQ==, magXml=RzJnfqV0PFYsC1ydkl143A==, pdfUrl=null, pdf=lOZpGEOkJFtXasM5ha84fg==, pdfFileSize=6597166, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=edpjL1/7cLr91VZHnJtl4A==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=9D8K6AvljrZZNtbDmD+YpQ==, mapNumber=null, fund=null)}, authors=[Author(id=1308841193782469197, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, orderNo=0, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1308841193866355279, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, 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Breed Sci, 2016, 66: 683-691., articleTitle=null, refAbstract=null), Reference(id=1308841203848798894, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=42, rfOrder=41, authorNames=null, journalName=null, refType=null, unstructuredReference=Xu Q, Huang Y, Deng XX. The definition, classification and evolution of Citrus based on whole genome sequence information [J]. Sci Sin Vitae (中国科学: 生命科学), 2024, 54: 525-536., articleTitle=null, refAbstract=null), Reference(id=1308841205534909103, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=43, rfOrder=42, authorNames=null, journalName=null, refType=null, unstructuredReference=Xin TY, Lou Q, Hao LJ, et al. DNA barcoding identification of commercial decoctions in traditional Chinese medicine [J]. 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J Guangdong Pharm Univ (广东药科大学学报), 2017, 33: 719-722., articleTitle=null, refAbstract=null)], funds=null, companyList=[AuthorCompany(id=1308841193543393862, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, xref=1, ext=[AuthorCompanyExt(id=1308841193555976775, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, companyId=1308841193543393862, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China), AuthorCompanyExt(id=1308841193576948296, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, companyId=1308841193543393862, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1中国医学科学院 北京协和医学院, 药用植物研究所, 中药资源教育部工程研究中心, 国家中医药管理局中药资源保护重点研究室, 北京 100193)]), AuthorCompany(id=1308841193669222985, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, xref=2, ext=[AuthorCompanyExt(id=1308841193677611594, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, companyId=1308841193669222985, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100193, China), AuthorCompanyExt(id=1308841193686000203, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, companyId=1308841193669222985, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2天然药物活性物质与功能国家重点实验室, 北京 100193)])], figs=[ArticleFig(id=1308841197850944117, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=vJEHTNlk3jTbYPJO7WQjug==, figureFileBig=edpjL1/7cLr91VZHnJtl4A==, tableContent=null), ArticleFig(id=1308841197913858678, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Fig.1, caption=Field records of Citrus germplasm growth status. 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The numerical values indicate the count of targets that have been experimentally confirmed in each species during this research, figureFileSmall=VHHEAsdcB0ieuX/k7fnNXQ==, figureFileBig=s4qMpgh6M83qXvVGQOPP4g==, tableContent=null), ArticleFig(id=1308841198278763129, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=d3YaFsaDtuTyEogZzMNxZg==, figureFileBig=zyqn4orD/AM6kNL9WGQM9Q==, tableContent=null), ArticleFig(id=1308841198337483386, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Fig.3, caption=Agarose gel electrophoresis and sequencing peak graphs results of specific target sequences for 11 Citrus species. M: DL1000 Marker; CK: Blank control, figureFileSmall=d3YaFsaDtuTyEogZzMNxZg==, figureFileBig=zyqn4orD/AM6kNL9WGQM9Q==, tableContent=null), ArticleFig(id=1308841198396203643, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=IEqMFe+Whg5iK7A6P7HnzQ==, figureFileBig=wn53iPAUmYrT/0vXeUfWRA==, tableContent=null), ArticleFig(id=1308841198454923900, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Fig.4, caption=Precise species identification of 11 Citrus species using CRISPR-Cas12a technology. Each group contains DNA from different species as the substrate. CK: Nuclease-free water, figureFileSmall=IEqMFe+Whg5iK7A6P7HnzQ==, figureFileBig=wn53iPAUmYrT/0vXeUfWRA==, tableContent=null), ArticleFig(id=1308841198513644157, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=ocQNiEh85X4+8CDaOoq2fw==, figureFileBig=IPBjo2urMT1lBfTD4aUEBw==, tableContent=null), ArticleFig(id=1308841198597530238, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Fig.5, caption=Agarose gel electrophoresis and specific target sequence alignment diagrams of Citri Reticulatae Semen crude drugs and decoction pieces. A: Agarose gel electrophoresis of PCR products amplified from Citri Reticulatae Semen crude drugs. 1-3: YC01-1-YC01-3; 4-6: YC02-1-YC02-3; 7-9: YC03-1-YC03-3; 10-12: YC04-1-YC04-3; 13-15: YC05-1-YC05-3; B: Agarose gel electrophoresis of PCR products amplified from Citri Reticulatae Semen decoction pieces. 16-18: YP01-1-YP01-3; 19-21: YP02-1-YP02-3; 22-24: YP03-1-YP03-3; 25-27: YP04-1-YP04-3; 28-30: YP05-1-YP05-3. M: DL1000 Marker; CK: blank control. C: Multiple sequence alignment of the amplified species-specific target sequences obtained from both Citri Reticulatae Semen crude drugs and decoction pieces. A dot (.) indicates that the nucleotide at this position is the same as in the reference sequence (YC01-1); bold letters indicate specific target sequences, figureFileSmall=ocQNiEh85X4+8CDaOoq2fw==, figureFileBig=IPBjo2urMT1lBfTD4aUEBw==, tableContent=null), ArticleFig(id=1308841198668833407, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesNCBI accessionSpeciesNCBI accession
Citrus australasicaGCA_029618575.1Citrus sinensisGCA_000695605.1
GCA_029618585.1GCA_018104345.1
GCA_030449855.1GCA_019143665.1
Citrus cavalerieiGCA_002013975.2GCA_019144155.1
GCA_030448935.1GCA_019144185.1
Citrus glaucaGCA_029633165.1GCA_019144225.1
GCA_029633175.1GCA_019144245.1
Citrus hindsiiGCA_004802465.1GCA_022201045.1
Citrus hongheensisGCA_030448925.1GCA_022201065.1
Citrus inodoraGCA_029618595.1GCA_033030525.1
GCA_029721495.1GCA_033030535.1
Citrus kinokuniGCA_033242385.1GCA_038048705.1
GCA_033242405.1GCA_041890265.1
GCA_033242425.1GCA_041890275.1
Citrus mangshanensisGCA_030449895.1GCA_963573335.1
Citrus maximaGCA_030448945.1GCA_019144195.1
GCA_002006925.1GCA_018105775.1
GCA_029641205.1GCA_000317415.1
Citrus medicaGCA_002013955.2Citrus trifoliataGCA_018350135.1
Citrus nobilisGCA_033242445.1Citrus unshiuGCA_002897195.1
GCA_033242465.1GCA_033242305.1
GCA_033242485.1GCA_033242325.1
Citrus reticulataGCA_003258625.1GCA_033242345.1
GCA_036169575.1
GCA_036169605.1
GCA_964263685.1
), ArticleFig(id=1308841198744330880, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Tab.1, caption=

Genomic information of Citrus genus

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SpeciesNCBI accessionSpeciesNCBI accession
Citrus australasicaGCA_029618575.1Citrus sinensisGCA_000695605.1
GCA_029618585.1GCA_018104345.1
GCA_030449855.1GCA_019143665.1
Citrus cavalerieiGCA_002013975.2GCA_019144155.1
GCA_030448935.1GCA_019144185.1
Citrus glaucaGCA_029633165.1GCA_019144225.1
GCA_029633175.1GCA_019144245.1
Citrus hindsiiGCA_004802465.1GCA_022201045.1
Citrus hongheensisGCA_030448925.1GCA_022201065.1
Citrus inodoraGCA_029618595.1GCA_033030525.1
GCA_029721495.1GCA_033030535.1
Citrus kinokuniGCA_033242385.1GCA_038048705.1
GCA_033242405.1GCA_041890265.1
GCA_033242425.1GCA_041890275.1
Citrus mangshanensisGCA_030449895.1GCA_963573335.1
Citrus maximaGCA_030448945.1GCA_019144195.1
GCA_002006925.1GCA_018105775.1
GCA_029641205.1GCA_000317415.1
Citrus medicaGCA_002013955.2Citrus trifoliataGCA_018350135.1
Citrus nobilisGCA_033242445.1Citrus unshiuGCA_002897195.1
GCA_033242465.1GCA_033242305.1
GCA_033242485.1GCA_033242325.1
Citrus reticulataGCA_003258625.1GCA_033242345.1
GCA_036169575.1
GCA_036169605.1
GCA_964263685.1
), ArticleFig(id=1308841198840799873, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Sample typeSample IDNameLocation
LeafCL01Citrus australasicaCRI
CL02Citrus cavalerieiCRI
CL03Citrus kinokuniCRI
CL04Citrus mangshanensisCRI
CL05Citrus maximaCRI
CL06Citrus medicaCRI
CL07Citrus reticulataCRI
CL08Citrus sinensisCRI
CL09Citrus trifoliataCRI
CL10Citrus unshiuCRI
CL11Citrus hongheensisCRI
Crude drugYC01-1Citri Reticulatae SemenGuangdong
YC01-2Citri Reticulatae SemenGuangdong
YC01-3Citri Reticulatae SemenGuangdong
YC02-1Citri Reticulatae SemenFujian
YC02-2Citri Reticulatae SemenFujian
YC02-3Citri Reticulatae SemenFujian
YC03-1Citri Reticulatae SemenGuangdong
YC03-2Citri Reticulatae SemenGuangdong
YC03-3Citri Reticulatae SemenGuangdong
YC04-1Citri Reticulatae SemenHunan
YC04-2Citri Reticulatae SemenHunan
YC04-3Citri Reticulatae SemenHunan
YC05-1Citri Reticulatae SemenZhejiang
YC05-2Citri Reticulatae SemenZhejiang
YC05-3Citri Reticulatae SemenZhejiang
Decoction piecesYP01-1Citri Reticulatae SemenBeijing
YP01-2Citri Reticulatae SemenBeijing
YP01-3Citri Reticulatae SemenBeijing
YP02-1Citri Reticulatae SemenGuangdong
YP02-2Citri Reticulatae SemenGuangdong
YP02-3Citri Reticulatae SemenGuangdong
YP03-1Citri Reticulatae SemenHunan
YP03-2Citri Reticulatae SemenHunan
YP03-3Citri Reticulatae SemenHunan
YP04-1Citri Reticulatae SemenJiangxi
YP04-2Citri Reticulatae SemenJiangxi
YP04-3Citri Reticulatae SemenJiangxi
YP05-1Citri Reticulatae SemenGuangdong
YP05-2Citri Reticulatae SemenGuangdong
YP05-3Citri Reticulatae SemenGuangdong
), ArticleFig(id=1308841198928880258, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Tab.2, caption=

Source of experimental materials. CRI: National Citrus Germplasm Repository Chongqing China, Citrus Research Institute, Chinese Academy of Agricultural Sciences

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Sample typeSample IDNameLocation
LeafCL01Citrus australasicaCRI
CL02Citrus cavalerieiCRI
CL03Citrus kinokuniCRI
CL04Citrus mangshanensisCRI
CL05Citrus maximaCRI
CL06Citrus medicaCRI
CL07Citrus reticulataCRI
CL08Citrus sinensisCRI
CL09Citrus trifoliataCRI
CL10Citrus unshiuCRI
CL11Citrus hongheensisCRI
Crude drugYC01-1Citri Reticulatae SemenGuangdong
YC01-2Citri Reticulatae SemenGuangdong
YC01-3Citri Reticulatae SemenGuangdong
YC02-1Citri Reticulatae SemenFujian
YC02-2Citri Reticulatae SemenFujian
YC02-3Citri Reticulatae SemenFujian
YC03-1Citri Reticulatae SemenGuangdong
YC03-2Citri Reticulatae SemenGuangdong
YC03-3Citri Reticulatae SemenGuangdong
YC04-1Citri Reticulatae SemenHunan
YC04-2Citri Reticulatae SemenHunan
YC04-3Citri Reticulatae SemenHunan
YC05-1Citri Reticulatae SemenZhejiang
YC05-2Citri Reticulatae SemenZhejiang
YC05-3Citri Reticulatae SemenZhejiang
Decoction piecesYP01-1Citri Reticulatae SemenBeijing
YP01-2Citri Reticulatae SemenBeijing
YP01-3Citri Reticulatae SemenBeijing
YP02-1Citri Reticulatae SemenGuangdong
YP02-2Citri Reticulatae SemenGuangdong
YP02-3Citri Reticulatae SemenGuangdong
YP03-1Citri Reticulatae SemenHunan
YP03-2Citri Reticulatae SemenHunan
YP03-3Citri Reticulatae SemenHunan
YP04-1Citri Reticulatae SemenJiangxi
YP04-2Citri Reticulatae SemenJiangxi
YP04-3Citri Reticulatae SemenJiangxi
YP05-1Citri Reticulatae SemenGuangdong
YP05-2Citri Reticulatae SemenGuangdong
YP05-3Citri Reticulatae SemenGuangdong
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SpeciesNumber of candidate targetsValidated specific target sequences in the target species (5′→3′)Chromosomal locationcrRNA (5′→3′)
Citrus australasica76 274Cau1:CTTTCATAGCTGGAGGTGTTACAAA//
Cau2:AAAAACAGGCCCATCATGGTAGAAA/UAAUUUCUACUAAGUGUAGAUUACCAUGAUGGGCCUGUUUUU
Cau3:TACATGCCTATTTGATACGACTAAA//
Citrus cavaleriei93 758Cca1:ATATGCACCCACACCAGGCCTTAAA//
Cca2:TAACCGATCGTCCGATCATAATAAA/UAAUUUCUACUAAGUGUAGAUUUAUGAUCGGACGAUCGGUUA
Citrus hongheensis353 002Cho1:CCATGGCTATGGTGCCCATACCAAA/UAAUUUCUACUAAGUGUAGAUGUAUGGGCACCAUAGCCAUGG
Citrus kinokuni1 318Cki1:TTATACCATAGCTACGCCTTTTAAA//
Cki2:CGACAACAAATGAAATCGCCAGAAA/UAAUUUCUACUAAGUGUAGAUUGGCGAUUUCAUUUGUUGUCG
Cki3:TAATGACAATCACGACACTATCAAA//
Citrus mangshanensis180 456Cman1:AGCAAATTGTGTGCGACTAAGGAAA/UAAUUUCUACUAAGUGUAGAUCUUAGUCGCACACAAUUUGCU
Cman2:GCATGGAAGCTAACCGAGCAACAAA//
Citrus maxima17 135Cmax1:TTAGCACCCTCCGCCTCTGTTCAAAChromosome 9/
Cmax2:CGATCGGTAACGCCCGTTGCCCAAAChromosome 4/
Cmax3:TAGCAGTACCCAGTGTAATCATAAAChromosome 4UAAUUUCUACUAAGUGUAGAUUGAUUACACUGGGUACUGCUA
Citrus medica62 598Cme1:GGCGTGGGTTAAGGAAAGATCTAAA//
Cme2:ACCCAGAAGTCTAACAGTCAGTAAA/UAAUUUCUACUAAGUGUAGAUCUGACUGUUAGACUUCUGGGU
Citrus reticulata4 838Cre1:GATCTGTAGGAGCGTTTGCAATAAAChromosome 5UAAUUUCUACUAAGUGUAGAUUUGCAAACGCUCCUACAGAUC
Cre2:AGGCTAGTCAGCTTTGCATTACAAAChromosome 5/
Citrus sinensis987Csi1:CAGACCCATGTTTCGTCAACCGAAAChromosome 2/
Csi2:CTGGCTACTCAACCAGAATTTTAAAChromosome 2/
Csi3:TTAGTTAGTGCTCATTCCCGAGAAAChromosome 4/
Csi4: CGTGGCATGTACAAACCCTCTCAAAChromosome 1UAAUUUCUACUAAGUGUAGAUAGAGGGUUUGUACAUGCCACG
Citrus trifoliata142 617Ctr1: AGAAATGATGGCTTAAGGTTTCAAAChromosome 1/
Ctr2:CAAATGGCAACTATGACTCCCCAAAChromosome 4UAAUUUCUACUAAGUGUAGAUGGGAGUCAUAGUUGCCAUUUG
Citrus unshiu243Cun1:TTACGGGGCTCCTCCAATTACCAAA//
Cun2:TCGCCATATGGACGCCGTTTGCAAA//
Cun3:TACACCCCGGGAATGGCCGGACAAA//
Cun4:TTGGCATCCGAAGGCGCCCGTCAAA//
Cun5:TGACGCAACGAATTCCCAATGGAAA/UAAUUUCUACUAAGUGUAGAUCAUUGGGAAUUCGUUGCGUCA
), ArticleFig(id=1308841199100846724, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308841190074704441, language=CN, label=Tab.3, caption=

Bioinformatics statistical results of species-specific target sequences in 11 Citrus species and crRNA. /: Not available; crRNA: CRISPR RNA, the RNA molecule that pairs complementarily with the target DNA sequence to be cleaved

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesNumber of candidate targetsValidated specific target sequences in the target species (5′→3′)Chromosomal locationcrRNA (5′→3′)
Citrus australasica76 274Cau1:CTTTCATAGCTGGAGGTGTTACAAA//
Cau2:AAAAACAGGCCCATCATGGTAGAAA/UAAUUUCUACUAAGUGUAGAUUACCAUGAUGGGCCUGUUUUU
Cau3:TACATGCCTATTTGATACGACTAAA//
Citrus cavaleriei93 758Cca1:ATATGCACCCACACCAGGCCTTAAA//
Cca2:TAACCGATCGTCCGATCATAATAAA/UAAUUUCUACUAAGUGUAGAUUUAUGAUCGGACGAUCGGUUA
Citrus hongheensis353 002Cho1:CCATGGCTATGGTGCCCATACCAAA/UAAUUUCUACUAAGUGUAGAUGUAUGGGCACCAUAGCCAUGG
Citrus kinokuni1 318Cki1:TTATACCATAGCTACGCCTTTTAAA//
Cki2:CGACAACAAATGAAATCGCCAGAAA/UAAUUUCUACUAAGUGUAGAUUGGCGAUUUCAUUUGUUGUCG
Cki3:TAATGACAATCACGACACTATCAAA//
Citrus mangshanensis180 456Cman1:AGCAAATTGTGTGCGACTAAGGAAA/UAAUUUCUACUAAGUGUAGAUCUUAGUCGCACACAAUUUGCU
Cman2:GCATGGAAGCTAACCGAGCAACAAA//
Citrus maxima17 135Cmax1:TTAGCACCCTCCGCCTCTGTTCAAAChromosome 9/
Cmax2:CGATCGGTAACGCCCGTTGCCCAAAChromosome 4/
Cmax3:TAGCAGTACCCAGTGTAATCATAAAChromosome 4UAAUUUCUACUAAGUGUAGAUUGAUUACACUGGGUACUGCUA
Citrus medica62 598Cme1:GGCGTGGGTTAAGGAAAGATCTAAA//
Cme2:ACCCAGAAGTCTAACAGTCAGTAAA/UAAUUUCUACUAAGUGUAGAUCUGACUGUUAGACUUCUGGGU
Citrus reticulata4 838Cre1:GATCTGTAGGAGCGTTTGCAATAAAChromosome 5UAAUUUCUACUAAGUGUAGAUUUGCAAACGCUCCUACAGAUC
Cre2:AGGCTAGTCAGCTTTGCATTACAAAChromosome 5/
Citrus sinensis987Csi1:CAGACCCATGTTTCGTCAACCGAAAChromosome 2/
Csi2:CTGGCTACTCAACCAGAATTTTAAAChromosome 2/
Csi3:TTAGTTAGTGCTCATTCCCGAGAAAChromosome 4/
Csi4: CGTGGCATGTACAAACCCTCTCAAAChromosome 1UAAUUUCUACUAAGUGUAGAUAGAGGGUUUGUACAUGCCACG
Citrus trifoliata142 617Ctr1: AGAAATGATGGCTTAAGGTTTCAAAChromosome 1/
Ctr2:CAAATGGCAACTATGACTCCCCAAAChromosome 4UAAUUUCUACUAAGUGUAGAUGGGAGUCAUAGUUGCCAUUUG
Citrus unshiu243Cun1:TTACGGGGCTCCTCCAATTACCAAA//
Cun2:TCGCCATATGGACGCCGTTTGCAAA//
Cun3:TACACCCCGGGAATGGCCGGACAAA//
Cun4:TTGGCATCCGAAGGCGCCCGTCAAA//
Cun5:TGACGCAACGAATTCCCAATGGAAA/UAAUUUCUACUAAGUGUAGAUCAUUGGGAAUUCGUUGCGUCA
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基于时珍法的柑橘属药用物种鉴定研究
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张娜娜 1 , 甘雨桐 1 , 辛天怡 1 , 史志杰 1 , 许文杰 1 , 宋经元 1, 2, *
药学学报 | 研究论文 2026,61(5): 1841-1851
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药学学报 |研究论文 2026 , 61 (5) : 1841 -1851
基于时珍法的柑橘属药用物种鉴定研究
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张娜娜1, 甘雨桐1, 辛天怡1, 史志杰1, 许文杰1, 宋经元1, 2, *
作者信息
  • 1中国医学科学院 北京协和医学院, 药用植物研究所, 中药资源教育部工程研究中心, 国家中医药管理局中药资源保护重点研究室, 北京 100193
  • 2天然药物活性物质与功能国家重点实验室, 北京 100193
通讯作者:
宋经元, Tel: 86-10-57833199, E-mail:
作者简介:

作者贡献:

张娜娜负责实验设计、样本收集、实验工作、数据分析、文章撰写及修改; 甘雨桐负责数据管理及分析, 参与实验工作和稿件修改; 辛天怡负责稿件修改; 史志杰参与实验工作和稿件修改; 许文杰参与稿件修改; 宋经元负责实验设计、总体把关和稿件修改等工作。

Analysis of whole-GEnome for medicinal species identification of Citrus
Na-na ZHANG1, Yu-tong GAN1, Tian-yi XIN1, Zhi-jie SHI1, Wen-jie XU1, Jing-yuan SONG1, 2, *
Affiliations
  • 1Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
  • 2State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100193, China
出版时间: 2026-05-12 doi: 10.16438/j.0513-4870.2025-1377
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柑橘属植物是世界上广泛种植的经济作物, 具有显著的药用价值和经济价值。然而, 由于柑橘属遗传背景高度复杂, 该属药用物种的准确鉴定面临挑战。本研究基于全基因组分析法(analysis of whole-GEnome, AGE), 又称为时珍法, 对柑橘属15个物种的49个基因组进行生物信息学分析, 成功构建涵盖15个物种的候选特异靶标序列库, 各物种靶标序列数量主要集中在10 000~100 000条之间。从候选特异靶标序列库中为相应物种选取特异靶标序列, 并通过Sanger测序和CRISPR-Cas12a技术证实选取的特异靶标序列具有高度特异性, 可有效鉴定柑橘属药用物种。在此基础上构建基于时珍法的柑橘属近缘物种鉴定体系, 实现30份市售橘核药材及饮片的准确鉴定。本研究证明时珍法可用于柑橘属药用物种的准确鉴定, 突破传统鉴定方法的瓶颈, 有效解决柑橘属药用物种的鉴定难题, 为中药材质量控制和临床用药安全提供技术支撑。

柑橘属  /  时珍法  /  生物信息学分析  /  特异靶标序列  /  药用物种鉴定

Citrus plants are economically and medicinally important crops worldwide. However, due to the highly complex genetic background of the genus, the accurate identification of medicinal species within this genus remains a major challenge. In this study, we employed the analysis of whole-GEnome (AGE), also known as the Shizhen Method, to conduct bioinformatics analysis on 49 genomes from 15 Citrus species, successfully constructing a candidate species-specific target sequence library that covers these species. The number of specific target sequences per species predominantly ranges from 10 000 to 100 000. From this candidate library, species-specific target sequences were selected for the corresponding species. Their high specificity was subsequently verified using Sanger sequencing and CRISPR-Cas12a technology, which confirmed their efficacy in identifying medicinal Citrus species. Based on this foundation, we established an AGE-based identification system for closely related Citrus species, which enabled the precise authentication of 30 commercial samples of Citri Reticulatae Semen and its decoction pieces. This study demonstrates that the AGE can be used for the accurate identification of medicinal Citrus species, which breaks through the bottlenecks of traditional methods and effectively resolves the identification challenges. It thereby provides technical support for quality control of Chinese herbal medicine and clinical medication safety.

Citrus  /  analysis of whole-GEnome  /  bioinformatics analysis  /  specific target sequences  /  medicinal species identification
张娜娜, 甘雨桐, 辛天怡, 史志杰, 许文杰, 宋经元. 基于时珍法的柑橘属药用物种鉴定研究. 药学学报, 2026 , 61 (5) : 1841 -1851 . DOI: 10.16438/j.0513-4870.2025-1377
Na-na ZHANG, Yu-tong GAN, Tian-yi XIN, Zhi-jie SHI, Wen-jie XU, Jing-yuan SONG. Analysis of whole-GEnome for medicinal species identification of Citrus[J]. Acta Pharmaceutica Sinica, 2026 , 61 (5) : 1841 -1851 . DOI: 10.16438/j.0513-4870.2025-1377
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柑橘属(Citrus L.)系芸香科(Rutaceae)柑橘亚科(Aurantioideae)植物[1], 作为世界上最重要的经济作物之一, 在140多个国家和地区有种植, 广泛分布于热带、亚热带和温带地区[2]。中国是柑橘属植物的重要的起源地之一, 栽培历史悠久、品种繁多, 拥有丰富的野生和栽培种质资源[3]。柑橘属植物是重要的药食同源植物。已有大量研究表明, 柑橘属植物具有显著的药用价值, 功能成分主要包括类黄酮[4]、香豆素[5]、生物碱等[6], 具有抗氧化[7]、抗炎[8, 9]、抗病毒[10]、抗癌[11]、降血压和降胆固醇[12, 13]、预防糖尿病[14, 15]、止咳化痰[16]、神经保护[17, 18]等多种生物活性。2025年国家卫生部发布的最新《药食同源物品目录》显示, 代代花、佛手、香橼、陈皮、橘红和化橘红均来自柑橘属。
由于柑橘属存在广泛的杂交、无性繁殖以及形态多样性, 其近缘物种的准确鉴定面临挑战。目前, 柑橘属物种鉴定方法主要包括形态鉴定[19, 20]、显微鉴定[21, 22]、理化鉴定[23]以及分子鉴定[24-27]。Nurzaman等[28]基于形态学和解剖学数据对柑橘属7种植物进行表型分析, 未能有效区分C. reticulata 'Dekopon'与C. sinensis 'Sunkist', 数量有限的表型性状难以全面代表基因组水平的本质差异, 容易受到主观判断的影响, 进行物种鉴定时可能出现偏差。Wang等[29]应用广泛靶向代谢组方法区分C. reticulata 'DHP'和C. reticulata 'BZH', 但该方法依赖于UPLC-ESI-MS/MS等高端仪器和自建数据库, 设备昂贵, 对实验条件和技术人员要求严格, 且样本前处理步骤繁琐, 不易普及。以DNA条形码为代表的分子鉴定方法对近缘物种和存在广泛种内变异物种的鉴定同样存在挑战[24-26]。Yu[26]对6属柑橘类近缘植物的分子鉴定研究证实, 无论是单一片段(ITS最佳, 鉴定率 < 60%)还是多片段组合, 无法实现所有类群的完全区分。因此, 亟需开发一种能够克服现有方法的局限性、兼具高分辨率和高通量特性的新技术, 以解决柑橘药用物种鉴定的难题。
本团队创建基于全基因组分析的物种鉴定新方法——AGE法(analysis of whole-GEnome), 又称为时珍法。该方法从物种全基因组寻找特异靶标序列, 精准识别特异靶标序列以实现物种的准确鉴定[30]。目前, 时珍法已成功应用于植物[31, 32]、动物[33]、真菌[34-37]的近缘物种的鉴定, 具有快速、准确的特点。因此, 本研究拟将时珍法应用于柑橘属药用物种鉴定研究, 对柑橘属15个物种的49个基因组进行分析, 并对极具药用价值的中药材基原物种——柑橘(Citrus reticulata)、柚(Citrus maxima)、香橼(Citrus medica)、甜橙(Citrus sinensis)、温州蜜柑(Citrus unshiu)等11个近缘物种进行实验验证, 为解决柑橘属药用物种鉴定难题、柑橘种质资源科学管理等提供新的技术手段, 同时也为柑橘属药材混伪品鉴定提供新思路。
材料与方法
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物种基因组信息   本研究共涉及柑橘属15个物种49个全基因组(下载于2024年11月15日), 均下载自NCBI基因组数据库(https://www.ncbi.nlm.nih.gov/), 详见表1。所用基因组由华中农业大学、Kazusa DNA Research Institute、University of California Riverside等机构发布。
实验材料   对应NCBI下载的基因组的柑橘属15个物种, 其中11个物种样品(图1)采自中国农业科学院国家果树种质重庆柑桔圃(National Citrus Germplasm Repository Chongqing China, Citrus Research Institute, Chinese Academy of Agricultural Sciences, CRI)。其余4个物种Citrus hindsii、Citrus glauca、Citrus nobilis和Citrus inodora由于种质资源限制未采集到样品。另自北京市、广东省、江西省、浙江省、湖南省和福建省等地购买市售橘核药材及饮片共30份, 详见表2。
试剂   50×TAE缓冲液(北京索莱宝科技有限公司); 2×Taq PCR Master Mix (北京艾德莱生物科技有限公司); BIOWEST琼脂糖Agarose G-10 (北京艾普立邦科技有限公司); DNA Marker DL1000 [宝日医生物技术(北京)有限公司]; PCR引物由天一辉远生物科技有限公司合成; DP305型天根植物DNA提取试剂盒[天根生化科技(北京)有限公司]; 成簇规律间隔短回文重复序列RNA (clustered regularly interspaced short palindromic repeats RNA, crRNA)和单链DNA (single strand DNA, ssDNA)均由金斯瑞(江苏)有限责任公司合成。
仪器   PL203型电子天平[梅特勒-托利多仪器(上海)有限公司]; Pad3-H型加热制冷型金属浴[卡尤迪生物科技(北京)有限公司]; 5424R型台式高速冷冻离心机和5430R型台式高速冷冻离心机(Eppendorf公司); DYY-8C型电泳仪(北京市六一仪器厂); 混合型震荡组织研磨仪(莱驰公司, 德国); Nanodrop 2000C分光光度计(赛默飞科学有限公司, 美国)。
基因组DNA提取   使用天根植物DNA提取试剂盒(DP305)提取基因组DNA, 用Nanodrop 2000C分光光度计测定DNA浓度, 加入适量ddH2O稀释成等浓度的DNA母液, 于-20 ℃保存备用。
生物信息学分析构建物种特异靶标序列库   使用AGE1.0 (注册号: 2025SR0250433)将柑橘属15个物种49个基因组(表1)分割为25 bp片段, 随后提取包含间隔序列相邻基序(protospacer adjacent motif, PAM)的序列(以TTTV开头或VAAA结尾)的片段(V代表A, G或C)。随后, 进一步筛选出同时包含A、G、C、T四种碱基且不含多聚体(poly)结构的特异性靶标序列。对目标物种包含PAM序列的25 bp片段与分析范围内其他物种的包含PAM序列的25 bp片段进行比对, 选择除PAM序列外的21 bp与其他物种序列存在有3个以上核苷酸差异或1个插入缺失的序列, 从而构建柑橘属物种特异靶标序列库。
基于BLAST的候选靶标序列特异性验证   从特异靶标序列库中挑选特异靶标序列, 首先依据靶标在候选库中的频次高低依次选取。在NCBI非冗余核苷酸数据库中进行BLAST比对, 根据物种特异靶标序列的筛选原则: 一是目标物种特异靶标序列与其他物种相比没有比对到PAM序列; 二是除PAM序列外的21-mer与其他物种序列存在有3个核苷酸以上差异或1个插入缺失。根据BLAST比对结果, 保留符合筛选原则的靶标序列。通过PCR扩增及Sanger测序, 验证靶标序列是否存在于对应物种基因组中。在此基础上, 优先选择特异性扩增且测序质量较高的特异靶标序列, 进行后续的特异性验证。实际操作中, 只需找到一条特异靶标序列就能够实现物种鉴定的目的。
基于Sanger测序验证特异性靶标序列   使用NCBI Primer-BLAST工具(https://www.ncbi.nlm.nih.gov/tools/primer-blast/)设计靶标序列上下游特异性引物, 引物长度为20~25 bp, Tm值设定为59 ± 2 ℃, GC含量45%~55%, 预期产物长度200~600 bp。以柑橘属物种DNA为模板进行PCR扩增, PCR扩增反应体系均为25 μL, 包括2×Taq Master Mix 12.5 μL, 上下游引物(10 µmol·L-1)各1 μL, 基因组DNA 2 μL (10 ng·μL-1)和灭菌双蒸水8.5 μL。以等体积的灭菌双蒸水替代模板DNA设置阴性对照。扩增程序为94 ℃, 5 min; 94 ℃, 30 s, 58 ℃, 30 s, 72 ℃, 45 s, 共30个循环; 72 ℃, 10 min。配置1.2%琼脂糖凝胶检测PCR扩增结果, 电泳条件为120 V、30 min, 并与DL1000 Marker对比, 确定扩增目的条带的大小, 将扩增成功的PCR产物利用ABI3730XL测序仪进行双向测序。使用CodonCode Aligner 10.0.3 (CodonCode Co., 美国)进行序列拼接, 拼接后的序列使用MEGA 7.0 (Molecular evolutionary genetics analysis)进行特异靶标序列比对。评估PCR扩增结果及Sanger测序结果, 筛选能在各目标物种中实现特异性扩增且测序质量高的靶标序列。
基于CRISPR-Cas12a系统验证特异性靶标序列   合成靶标特异性crRNA, 通过CRISPR-Cas12a系统实现可视荧光检测。采用50 μL体系, 其中含有5 μL 10×NEBuffer 2.1、1 μL Cas12a (33 nmol·L-1)、1.65 μL crRNA (300 nmol·L-1)、10 μL底物DNA, 2 μL ssDNA (/5′ 6-FAM/CCCCCCCCCC/3′ BHQ-1, 400 nmol·L-1)和30.35 μL灭菌双蒸水。首先将Cas12a和crRNA及DNA底物在37 ℃下1×NEBuffer中孵育10 min。之后, 向孵育后的混合液中加入ssDNA, 最后通过蓝光透射仪[BG-Vtrans520s, 196 Baygene Biotech (Beijing) Co., Ltd., 中国] 直接观察荧光现象, 拍摄时采用参数: 光圈ƒ/1.6, 曝光时间1/30 s, ISO 1 000, 曝光补偿0 eV。
特异靶标序列在柑橘属药材及饮片中的应用   从广东等6个省市收集橘核药材及饮片共30份, 进行特异靶标序列的检测。以橘核药材及饮片的基因组DNA为模板, 使用特异性引物Cre1-F (5′-GCTACAAAGCG AAGCACACG-3′)和Cre1-R (5′-AGCCATTGTCGAAG CACTGA-3′)进行PCR扩增, 反应体系与程序同植物样本验证过程。测序结果使用CodonCode Aligner 10.0.3 (CodonCode Co., 美国)进行序列拼接, 拼接后的序列使用MEGA 7.0 (molecular evolutionary genetics analysis)进行特异靶标序列比对。
结果
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1　柑橘属物种特异靶标序列库的构建
通过对柑橘属15个物种的49个基因组进行生物信息学分析, 成功构建柑橘属物种候选特异靶标序列库。统计结果分析表明, 分析范围内的物种候选特异靶标序列数量从最低的243条(温州蜜柑C. unshiu)到最高的353 002条(红河橙C. hongheensis)相差近1 500倍, 特异靶标序列数量大多集中在10 000条到100 000条之间(图2)。从数量上看, 时珍法为柑橘属药用物种鉴定提供了丰富的候选特异靶标序列。从候选特异靶标序列库中为11个物种挑选4~50条特异靶标序列, 共计186条, BLAST结果显示各物种符合筛选原则的特异靶标数量在4~46条之间, 共计158条, 占比约为85%。在此范围内, 分别挑选1~15条靶标, 在目标物种中进行实验验证, 结合PCR扩增及Sanger测序结果, 各物种分别获得1~5条存在于对应物种基因组中的特异靶标序列(表3), 从中为各物种挑选1条进行后续的特异性验证。
对上述特异靶标序列在各自对应物种基因组中查询, 发现上述特异靶标序列均未进行功能注释, 其中仅11条具有染色体定位信息(表3)。
2　琼脂糖凝胶电泳及Sanger测序均可验证靶标序列特异性
对柑橘属11个物种异靶标序列进行特异性实验验证。通过PCR扩增联合琼脂糖凝胶电泳的方法进行检测, 结果显示, 特异靶标序列扩增产物均符合预期大小且仅在目标物种中扩增成功而非目标物种没有扩增成功, 表现出高度的特异性。采用Sanger测序技术对特异靶标序列进行检测。测序数据显示, 成功在目标物种中检测到相应的特异靶标序列。这些特异靶标序列的测序质量高且能够在目标物种中完全匹配(图3), 进一步说明这11条的靶标序列具有高度的特异性, 能够准确鉴定目标物种。
3　基于CRISPR-Cas12a系统验证靶标序列特异性
利用CRISPR-Cas12a技术对柑橘属植物的特异靶标序列进行检测。与测序结果一致, CRISPR-Cas12a系统成功实现对11个物种特异靶标序列的特异性检测。结果显示, 只有目标物种能够产生明显的荧光信号, 而在非目标物种未观察到明显的荧光信号(图4)。这表明CRISPR-Cas12a系统能够有效鉴别目标物种且兼具便捷性和直观性的优点, 便于实时分析和现场检测。
4　基于特异靶标序列的柑橘属药材及饮片准确鉴定
利用橘核药材及饮片考察特异靶标序列的实际应用效果。以橘核药材及饮片DNA为模板, 以特异靶标上下游引物进行PCR扩增并通过琼脂糖凝胶电泳进行检测, 结果显示在30份样品中均扩增得到单一清晰的条带(图5)。采用Sanger测序技术对PCR产物进行检测。测序数据显示, 成功在30份待检样品中检测到一致的特异靶标序列, 与其基原物种Citrus reticulata的特异靶标序列一致, 实现橘核药材及饮片的准确鉴定。
讨论
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本研究首次将时珍法应用于柑橘属药用物种鉴定。通过建立覆盖柑橘(C. reticulata)、柚(C. maxima)、香橼(C. medica)等药用物种的靶标序列库, 成功构建柑橘属近缘物种鉴定体系, 该体系辐射到约80%的柑橘属中药材。结果表明, 筛选所得11条特异靶标序列表现出高度的特异性, 可实现柑橘属药用物种的准确鉴定。其中, Sanger测序可直接反映特异靶标序列差异情况, 而通过CRISPR-Cas12a系统可实现对特异靶标序列的特异性检测, 且可通过荧光实现可视化。目前CRISPR-Cas12a多用于柑橘病原体(如细菌、真菌)检测[38-40], 尚无文献报道其在柑橘属物种鉴定中的系统应用。已有研究通过基因组分析揭示了部分柑橘属物种间的亲缘关系, Fujii等[41]通过基因组分析揭示纪州蜜橘(C. kinokuni)作为温州蜜柑(C. unshiu)母本的关系, Xu等[42]提出柚(C. maxima)和红河橙(C. hongheensis)具有较近的亲缘关系。通过AGE1.0分析获得的特异靶标序列, 可实现对上述物种的准确鉴定, 且适配Sanger测序、高通量测序、CRISPR、琼脂糖凝胶电泳等多种实验技术[30]。由此可见, 时珍法能突破亲缘关系密切物种的鉴定瓶颈, 为近缘物种的精确鉴别提供可靠技术手段。
时珍法可在遗传背景复杂的近缘物种中实现准确鉴定, 同时完成从生物信息学分析到市售药材及饮片实践应用的验证。这依赖于时珍法的底层逻辑——不同物种基因组序列必然存在差异的原理, 确保特异靶标序列在目标物种中存在, 而在其他物种中不存在, 从而实现物种的精准鉴定[30]。基于时珍法, 本研究以30份橘核药材及饮片的准确基原鉴定为例, 充分展示了时珍法在中药鉴定领域的应用潜力, 为柑橘属药材如化橘红等的精准鉴定提供新方法。多项研究共同揭示药材DNA易降解给分子鉴定带来的挑战, Xin等[43]系统验证DNA条形码技术在市售饮片鉴定中的适用性, 其中橘核饮片因基因组DNA严重降解而无法获得PCR扩增产物, 性状鉴定因缺乏关键鉴别特征, 最终未能确定其基原物种。Cheng等[44]基于ITS2序列对广陈皮基原植物及药材进行DNA分子鉴定, 药材的测序成功率明显低于植物的测序成功率, 且呈现出随贮藏年份增加而递减的趋势。因此, 在应用时珍法鉴定此类药材时, 建议采取诸如将扩增子片段长度控制在200 bp以下[35]、优化PCR扩增体系与条件等针对性策略, 以有效提升在降解DNA样本中的扩增成功率。
时珍法与DNA条形码、SNP分型等现有分子鉴定方法相比, 在成本方面, 时珍法的前期开发需基于目标物种及其近缘种的基因组或测序数据构建候选靶标序列库, 该阶段涉及生物信息学分析与计算平台投入。但一旦靶标库建立, 其具体检测成本取决于所选技术路径, 具有较高灵活性。例如, 若采用PCR结合Sanger测序, 其单样本成本与DNA条形码相近; 而SNP分型通常需要通过重测序等方式筛选特异性位点, 其前期开发与检测成本一般高于DNA条形码方法。在通量方面, 时珍法可根据实际需求适配不同检测手段, 针对单一样本或现场快速筛查, 可采用可视化荧光或侧向流试纸条实现快速检测; 对于批量样本, 则可依托PCR扩增及Sanger测序进行通量分析, 或利用芯片、高通量测序平台进行。后者类似基于芯片或高通量测序平台的SNP分型技术的大规模样本高通量筛查。在适用场景方面, 时珍法除了在实验室环境下, 尤其适用于现场快速检测。例如, 结合CRISPR-Cas12a技术可在30 min内获得可视化检测结果[34, 37], 且无需依赖昂贵仪器, 显著提升了检测效率与现场适用性, 弥补了传统分子鉴定方法在快速响应与便携性方面的不足。
目前将柑橘属15个物种的49个基因组纳入分析, 仍存在一定局限。随着基因组学技术的发展, 更高质量和更多类型的柑橘基因组有望被组装和注释, 建议在此基础上进一步扩大柑橘属物种的分析范围, 同时将更多高质量柑橘属物种基因组纳入分析范畴。并将时珍法与人工智能相结合, 利用实验筛选获得的特异靶标序列训练AI模型, 进而利用成熟后的AI模型实现对海量序列的自动化、智能化筛选以提升效率。值得关注的是, 扩大分析范围将进一步提高时珍法对柑橘属物种鉴定的适用性: 一是物种数量的增加, 有助于实现在更宽泛的遗传背景下评估特异靶标序列的鉴定能力; 二是基因组数量的增多, 能够提供更全面的种内遗传变异信息, 从而筛选出在物种内部保守、种间差异显著的高特异性靶标。相较基因组较小、结构相对简单的真菌[34-37], 柑橘属基因组具有大小中等、重复序列含量高、杂合度高等特点, 而引物设计是实验成功的关键因素之一[35]。因此, 也需应对高杂合度和重复序列带来的技术挑战。一方面, 高重复序列导致候选靶标序列库中非特异性序列(如多聚体、简单重复序列)比例过高; 另一方面, 高杂合度则使得在目标物种内部难以找到种内保守的特异序列, 这两者共同增加了筛选有效靶标和设计稳定引物的难度。因此, 需从生物信息学筛选策略层面进行针对性优化。①针对高重复序列的靶标序列优化: 在生物信息学分析阶段, 设置更严格的序列过滤与筛选条件。在构建候选靶标数据库时, 进一步筛选出同时包含A、G、C、T四种碱基且不含多聚体(poly)结构的特异靶标序列; ②针对高杂合度的靶标筛选策略强化: 为应对高杂合度带来的挑战, 提高种内保守性要求, 设置更高的种内频率阈值, 过滤掉因杂合位点或测序不准确导致的存疑序列。通过整合这些优化的生物信息学筛选策略, 时珍法有望更有效地克服由基因组结构复杂性带来的障碍, 拓展其在具有复杂基因组特征的物种鉴定中的应用范围。
综上所述, 时珍法为柑橘属药用物种的准确鉴定、商品化药材的准确追溯与真伪鉴别提供有力的技术支撑, 也为保障橘核药材及其相关制剂的质量可控性与用药安全性奠定坚实基础。

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2026年第61卷第5期
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doi: 10.16438/j.0513-4870.2025-1377
  • 接收时间：2025-11-19
  • 首发时间：2026-09-21
  • 出版时间：2026-05-12
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  • 收稿日期：2025-11-19
  • 修回日期：2026-01-12
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    1中国医学科学院 北京协和医学院, 药用植物研究所, 中药资源教育部工程研究中心, 国家中医药管理局中药资源保护重点研究室, 北京 100193
    2天然药物活性物质与功能国家重点实验室, 北京 100193

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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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