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Article(id=1201124482615308418, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1201124478286786612, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2023-0691, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1685462400000, receivedDateStr=2023-05-31, revisedDate=1689868800000, revisedDateStr=2023-07-21, acceptedDate=null, acceptedDateStr=null, onlineDate=1764299992469, onlineDateStr=2025-11-28, pubDate=1710172800000, pubDateStr=2024-03-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1764299992469, onlineIssueDateStr=2025-11-28, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1764299992469, creator=13701087609, updateTime=1764299992469, updator=13701087609, issue=Issue{id=1201124478286786612, tenantId=1146029695717560320, journalId=1189982191388893191, year='2024', volume='59', issue='3', pageStart='493', pageEnd='788', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1764299991434, creator=13701087609, updateTime=1764300490467, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1201126571420639892, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1201124478286786612, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1201126571420639893, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1201124478286786612, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=764, endPage=774, ext={EN=ArticleExt(id=1201124483571609780, articleId=1201124482615308418, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Characterization and phylogenetic analysis of chloroplast genome of Cynanchum wallichii and Cynanchum otophyllum, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Cynanchum wallichii and Cynanchum otophyllum belong to the genus Cynanchum in the family Apocynaceae, and are important medicinal plants. In this study, we sequenced and assembled the chloroplast genomes of C. wallichii and C. otophyllum, and performed a phylogenetic analysis of the structural characteristics of their chloroplast genomes and their phylogenetic positions. The results showed that the chloroplast genomes of both C. wallichii and C. otophyllum had a typical tetrad structure, with 133 genes annotated, and the total GC contents of both were similar. Codon preference analysis showed that the relative synonymous codon usage in the chloroplast genomes of C. wallichii and C. otophyllum differed slightly, but the differences were not significant, and there was a strong A or U preference at the third codon position. In both chloroplast genomes, 91 and 103 simple sequence repeats were detected respectively, and the largest proportion of A/T type repeats. Nucleotide polymorphism analysis showed that the nucleotide diversity of the intergenic sequences in the chloroplast genome of genus Cynanchum were generally higher than those of the common gene sequences. A pair of primers was designed based on the high variation region of the chloroplast genome to identify C. wallichii and C. otophyllum. The phylogenetic analysis showed that the C. wallichii and Cynanchum thesioides were the closest relatives, while the C. otophyllum, Cynanchum bungei and Cynanchum wilfordii formed a stable monophyletic clade within the genus Cynanchum, and the three species were closely related. The comparative analysis of the chloroplast genomic characteristics and phylogeny of C. wallichii and C. otophyllum will provide a theoretical basis for the species identification of the two plants and for the study of genetic diversity and phylogeny of the genus Cynanchum.

, correspAuthors=Lan-ping ZHENG, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2024 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=Ying-min GENG, Xing-qian ZHOU, Ti-cao ZHANG, Lan-ping ZHENG), CN=ArticleExt(id=1201124485865894228, articleId=1201124482615308418, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=昆明杯冠藤与青羊参叶绿体基因组特征比较及系统发育分析, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

昆明杯冠藤和青羊参隶属于夹竹桃科鹅绒藤属, 是重要的药用植物。本研究对昆明杯冠藤和青羊参叶绿体基因组进行测序、组装, 并对两者叶绿体基因组的结构特征及其系统发育位置进行了分析。结果表明, 昆明杯冠藤和青羊参叶绿体基因组均具有典型的四分体结构, 注释到133个基因, 两者总GC含量接近。密码子偏好性分析显示, 昆明杯冠藤和青羊参叶绿体基因组中相对同义密码子使用度略有不同, 但差异不大, 且在密码子第3位有强烈的A或U偏好。在两者叶绿体基因组中分别检测到91个和103个简单重复序列, 以A/T类型重复占比最大。核苷酸多态性分析显示, 鹅绒藤属叶绿体基因组共有间区序列的核苷酸多态性值高于共有基因序列, 基于共有间区序列的高变区设计了一对引物可对昆明杯冠藤和青羊参进行鉴别。系统发育分析表明, 昆明杯冠藤和地梢瓜亲缘关系最近, 青羊参、白首乌和隔山消在鹅绒藤属中形成稳定的单系分支, 三者亲缘关系较近。对昆明杯冠藤和青羊参叶绿体基因组特征及其系统发育的比较分析将为两种植物的物种鉴定及鹅绒藤属植物的遗传多样性和系统进化研究奠定理论基础。

, correspAuthors=郑兰平, authorNote=null, correspAuthorsNote=
*郑兰平, E-mail:
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Acta Bot Yunnan (云南植物研究), 1989, 11: 41-50., articleTitle=null, refAbstract=null)], funds=[Fund(id=1201124494199976881, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, awardId=202301AT070254, language=CN, fundingSource=云南省基础研究项目(202301AT070254), fundOrder=null, country=null), Fund(id=1201124494296445880, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, awardId=202101AZ070001-056, language=CN, fundingSource=云南省应用基础研究中医联合专项(202101AZ070001-056), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1201124486146912621, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, xref=null, ext=[AuthorCompanyExt(id=1201124486159495534, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, companyId=1201124486146912621, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming 650500, China), AuthorCompanyExt(id=1201124486167884143, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, companyId=1201124486146912621, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=云南中医药大学中药学院, 云南 昆明 650500)])], figs=[ArticleFig(id=1201124489900815036, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=EN, label=null, caption=null, figureFileSmall=HSapQ7RJ8f9K3P4I2H9kvg==, figureFileBig=2gBTPk+F0euvTnsNvEaNWg==, tableContent=null), ArticleFig(id=1201124490043421390, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Figure 1, caption= Map of chloroplast genome of <i>C. wallichii</i> and <i>C. otophyllum</i> , figureFileSmall=HSapQ7RJ8f9K3P4I2H9kvg==, figureFileBig=2gBTPk+F0euvTnsNvEaNWg==, tableContent=null), ArticleFig(id=1201124490299273955, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=EN, label=null, caption=null, figureFileSmall=PmSZlPWXB2nSGsVANLd5ig==, figureFileBig=f+Z86ZnlFQfox5TwLxNNbg==, tableContent=null), ArticleFig(id=1201124490420908783, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Figure 2, caption= Relative synonymous codon usage (RSCU) of <i>C. wallichii</i> (A) and <i>C. otophyllum</i> (B). 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No.SpeciesFromAccession
1Cynanchum wallichiiThis studyOQ198623
2Cynanchum otophyllumThis studyOQ928061
3Cynanchum bungeiNCBIOK271106
4Cynanchum thesioidesNCBIMW864598
5Cynanchum chinenseNCBINC_057432
6Cynanchum wilfordiiNCBINC_029459
7Cynanchum wilfordiiNCBIKX352467
8Cynanchum auriculatumNCBINC_029460
9Cynanchum auriculatumNCBIKU900231
10Cynanchum sibiricumNCBIOQ390041
11Vincetoxicum mongolicumNCBINC_065505
12Vincetoxicum forrestiiNCBINC_060305
13Vincetoxicum pycnostelmaNCBIOK271107
14Vincetoxicum versicolorNCBINC_052877
15Vincetoxicum lindleyiNCBINC_069945
16Vincetoxicum hainanenseNCBINC_051946
17Calotropis giganteaNCBINC_041431
18Calotropis proceraNCBINC_041440
19Asclepias syriacaNCBINC_022432
20Asclepias niveaNCBINC_022431
21Hoya pottsiiNCBINC_042246
22Hoya liangiiNCBINC_042245
23Hoya thomsoniiNCBINC_067612
24Hoya melifluaNCBINC_069571
25Gymnema sylvestreNCBINC_047175
26Pentasachme caudatumNCBIMW136321
27Apocynum pictumNCBINC_070061
28Apocynum venetumNCBINC_053902
29Nerium oleanderNCBINC_025656
), ArticleFig(id=1201124493226898292, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Table 1, caption=

List of selected species and their informations

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No.SpeciesFromAccession
1Cynanchum wallichiiThis studyOQ198623
2Cynanchum otophyllumThis studyOQ928061
3Cynanchum bungeiNCBIOK271106
4Cynanchum thesioidesNCBIMW864598
5Cynanchum chinenseNCBINC_057432
6Cynanchum wilfordiiNCBINC_029459
7Cynanchum wilfordiiNCBIKX352467
8Cynanchum auriculatumNCBINC_029460
9Cynanchum auriculatumNCBIKU900231
10Cynanchum sibiricumNCBIOQ390041
11Vincetoxicum mongolicumNCBINC_065505
12Vincetoxicum forrestiiNCBINC_060305
13Vincetoxicum pycnostelmaNCBIOK271107
14Vincetoxicum versicolorNCBINC_052877
15Vincetoxicum lindleyiNCBINC_069945
16Vincetoxicum hainanenseNCBINC_051946
17Calotropis giganteaNCBINC_041431
18Calotropis proceraNCBINC_041440
19Asclepias syriacaNCBINC_022432
20Asclepias niveaNCBINC_022431
21Hoya pottsiiNCBINC_042246
22Hoya liangiiNCBINC_042245
23Hoya thomsoniiNCBINC_067612
24Hoya melifluaNCBINC_069571
25Gymnema sylvestreNCBINC_047175
26Pentasachme caudatumNCBIMW136321
27Apocynum pictumNCBINC_070061
28Apocynum venetumNCBINC_053902
29Nerium oleanderNCBINC_025656
), ArticleFig(id=1201124493365310328, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesSample partNumberSample No.Location
C. wallichiiLeaf2BGTA-BBaoshan, Yunnan
C. otophyllumLeaf2QYSA-BLijiang, Yunnan
C. auriculatumRoot1FHCRFenghuang, Hunan
C. auriculatumStem2FHAS, FHBSFenghuang, Hunan
C. auriculatumLeaf2FHAL, FHBLFenghuang, Hunan
), ArticleFig(id=1201124493520499584, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Table 2, caption=

Samples used to verify the specific DNA barcode

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SpeciesSample partNumberSample No.Location
C. wallichiiLeaf2BGTA-BBaoshan, Yunnan
C. otophyllumLeaf2QYSA-BLijiang, Yunnan
C. auriculatumRoot1FHCRFenghuang, Hunan
C. auriculatumStem2FHAS, FHBSFenghuang, Hunan
C. auriculatumLeaf2FHAL, FHBLFenghuang, Hunan
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SpeciesGenomeLSCIRSSC
Length/bpG+C/%Length/bpG+C/%Length/bpG+C/%Length/bpG+C/%
C. wallichii159 80837.8790 90136.1523 98243.7020 94331.92
C. otophyllum161 05037.7992 00936.1324 60443.2119 83332.01
), ArticleFig(id=1201124493793129367, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Table 3, caption=

Composition and characteristic of chloroplast genome in C. wallichii and C. otophyllum

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesGenomeLSCIRSSC
Length/bpG+C/%Length/bpG+C/%Length/bpG+C/%Length/bpG+C/%
C. wallichii159 80837.8790 90136.1523 98243.7020 94331.92
C. otophyllum161 05037.7992 00936.1324 60443.2119 83332.01
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CategoryGene groupGene nameNumber
Gene for photosynthesisPhotosystem ⅠpsaA, psaB, psaC, psaI, psaJ5
Photosystem ⅡpsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ15
Cytochrome b/f complexpetA, petB, petD, petG, petL, petN6
NADH dehydrogenasendhA, ndhBa, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK12
Subunits of ATP synthaseatpA, atpB, atpE, atpF, atpH, atpI6
Rubisco large subunitsrbcL1
Self-replicationLange subunits of ribosomerpl2a, rpl14, rpl16, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl3611
Small subunits of ribosomerps2, rps3, rps4, rps7a, rps8, rps11, rps12a, rps14, rps15, rps16, rps18, rps1914
RNA polymeraserpoA, rpoB, rpoC1, rpoC24
Ribosomal RNA genesrrn4.5Sa, rrn5Sa, rrn16Sa, rrn23Sa8
Transfer RNA genestrnA-UGCa, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAUa, trnI-GAUa, trnK-UUU, trnL-CAAa, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUUa, trnP-UGG, trnQ-UUG, trnR-ACGa, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GACa, trnV-UAC, trnW-CCA, trnY-GUA37
Other genesProteaseclpP1
MaturasematK1
Translation initiation factorinfA1
Envelop membrane proteincemA1
Subunits of acety-CoA-carboxylaseaccD1
C-type cytochrome synthesisccsA1
Unknow geneHypothetical chloroplast reading framesycf1a, ycf2a, ycf3, ycf4, ycf15a8
Total133
), ArticleFig(id=1201124494036399013, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1201124482615308418, language=CN, label=Table 4, caption=

List of annotated genes in C. wallichii and C. otophyllum chloroplast genome. aIndicates that it contains two copies of genes

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CategoryGene groupGene nameNumber
Gene for photosynthesisPhotosystem ⅠpsaA, psaB, psaC, psaI, psaJ5
Photosystem ⅡpsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ15
Cytochrome b/f complexpetA, petB, petD, petG, petL, petN6
NADH dehydrogenasendhA, ndhBa, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK12
Subunits of ATP synthaseatpA, atpB, atpE, atpF, atpH, atpI6
Rubisco large subunitsrbcL1
Self-replicationLange subunits of ribosomerpl2a, rpl14, rpl16, rpl20, rpl22, rpl23a, rpl32, rpl33, rpl3611
Small subunits of ribosomerps2, rps3, rps4, rps7a, rps8, rps11, rps12a, rps14, rps15, rps16, rps18, rps1914
RNA polymeraserpoA, rpoB, rpoC1, rpoC24
Ribosomal RNA genesrrn4.5Sa, rrn5Sa, rrn16Sa, rrn23Sa8
Transfer RNA genestrnA-UGCa, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAUa, trnI-GAUa, trnK-UUU, trnL-CAAa, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUUa, trnP-UGG, trnQ-UUG, trnR-ACGa, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GACa, trnV-UAC, trnW-CCA, trnY-GUA37
Other genesProteaseclpP1
MaturasematK1
Translation initiation factorinfA1
Envelop membrane proteincemA1
Subunits of acety-CoA-carboxylaseaccD1
C-type cytochrome synthesisccsA1
Unknow geneHypothetical chloroplast reading framesycf1a, ycf2a, ycf3, ycf4, ycf15a8
Total133
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昆明杯冠藤与青羊参叶绿体基因组特征比较及系统发育分析
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耿应敏 , 周兴乾 , 张体操 , 郑兰平 *
药学学报 | 研究论文 2024,59(3): 764-774
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药学学报 | 研究论文 2024, 59(3): 764-774
昆明杯冠藤与青羊参叶绿体基因组特征比较及系统发育分析
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耿应敏, 周兴乾, 张体操, 郑兰平*
作者信息
  • 云南中医药大学中药学院, 云南 昆明 650500

通讯作者:

*郑兰平, E-mail:
Characterization and phylogenetic analysis of chloroplast genome of Cynanchum wallichii and Cynanchum otophyllum
Ying-min GENG, Xing-qian ZHOU, Ti-cao ZHANG, Lan-ping ZHENG*
Affiliations
  • College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming 650500, China
出版时间: 2024-03-12 doi: 10.16438/j.0513-4870.2023-0691
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摘要
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昆明杯冠藤和青羊参隶属于夹竹桃科鹅绒藤属, 是重要的药用植物。本研究对昆明杯冠藤和青羊参叶绿体基因组进行测序、组装, 并对两者叶绿体基因组的结构特征及其系统发育位置进行了分析。结果表明, 昆明杯冠藤和青羊参叶绿体基因组均具有典型的四分体结构, 注释到133个基因, 两者总GC含量接近。密码子偏好性分析显示, 昆明杯冠藤和青羊参叶绿体基因组中相对同义密码子使用度略有不同, 但差异不大, 且在密码子第3位有强烈的A或U偏好。在两者叶绿体基因组中分别检测到91个和103个简单重复序列, 以A/T类型重复占比最大。核苷酸多态性分析显示, 鹅绒藤属叶绿体基因组共有间区序列的核苷酸多态性值高于共有基因序列, 基于共有间区序列的高变区设计了一对引物可对昆明杯冠藤和青羊参进行鉴别。系统发育分析表明, 昆明杯冠藤和地梢瓜亲缘关系最近, 青羊参、白首乌和隔山消在鹅绒藤属中形成稳定的单系分支, 三者亲缘关系较近。对昆明杯冠藤和青羊参叶绿体基因组特征及其系统发育的比较分析将为两种植物的物种鉴定及鹅绒藤属植物的遗传多样性和系统进化研究奠定理论基础。

鹅绒藤属  /  叶绿体基因组  /  系统发育  /  高通量测序  /  DNA条形码

Cynanchum wallichii and Cynanchum otophyllum belong to the genus Cynanchum in the family Apocynaceae, and are important medicinal plants. In this study, we sequenced and assembled the chloroplast genomes of C. wallichii and C. otophyllum, and performed a phylogenetic analysis of the structural characteristics of their chloroplast genomes and their phylogenetic positions. The results showed that the chloroplast genomes of both C. wallichii and C. otophyllum had a typical tetrad structure, with 133 genes annotated, and the total GC contents of both were similar. Codon preference analysis showed that the relative synonymous codon usage in the chloroplast genomes of C. wallichii and C. otophyllum differed slightly, but the differences were not significant, and there was a strong A or U preference at the third codon position. In both chloroplast genomes, 91 and 103 simple sequence repeats were detected respectively, and the largest proportion of A/T type repeats. Nucleotide polymorphism analysis showed that the nucleotide diversity of the intergenic sequences in the chloroplast genome of genus Cynanchum were generally higher than those of the common gene sequences. A pair of primers was designed based on the high variation region of the chloroplast genome to identify C. wallichii and C. otophyllum. The phylogenetic analysis showed that the C. wallichii and Cynanchum thesioides were the closest relatives, while the C. otophyllum, Cynanchum bungei and Cynanchum wilfordii formed a stable monophyletic clade within the genus Cynanchum, and the three species were closely related. The comparative analysis of the chloroplast genomic characteristics and phylogeny of C. wallichii and C. otophyllum will provide a theoretical basis for the species identification of the two plants and for the study of genetic diversity and phylogeny of the genus Cynanchum.

Cynanchum  /  chloroplast genome  /  phylogeny  /  high-throughput sequencing  /  DNA barcode
耿应敏, 周兴乾, 张体操, 郑兰平. 昆明杯冠藤与青羊参叶绿体基因组特征比较及系统发育分析. 药学学报, 2024 , 59 (3) : 764 -774 . DOI: 10.16438/j.0513-4870.2023-0691
Ying-min GENG, Xing-qian ZHOU, Ti-cao ZHANG, Lan-ping ZHENG. Characterization and phylogenetic analysis of chloroplast genome of Cynanchum wallichii and Cynanchum otophyllum[J]. Acta Pharmaceutica Sinica, 2024 , 59 (3) : 764 -774 . DOI: 10.16438/j.0513-4870.2023-0691
正文
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鹅绒藤属(Cynanchum) 植物是我国重要的药用植物种质资源, 在常用中药和民间民族用药中应用广泛, 具有显著的资源优势[1]。昆明杯冠藤(Cynanchum wallichii Wight) 和青羊参(Cynanchum otophyllum Schneid.) 是夹竹桃科(Apocynaceae) 鹅绒藤属多年生草质藤本植物[2]。二者均以根入药, 分别称之为断节参和青阳参, 是我国独具特色的民族中药材, 药用历史悠久, 分别作为虎力散的组成药和青阳参片的原料药[3, 4]。
昆明杯冠藤和青羊参植物形态相似, 花、果期相近, 二者形态差异主要在于叶腋有无叶托, 花萼内部腺体个数以及蓇葖果形态, 这些微小的鉴别特征在野外或用肉眼无法准确分辨[2, 5]。昆明杯冠藤生长于山坡草地、村边和路旁灌木丛中或山谷等处, 产于云南、贵州、广西和四川等省区[2]。青羊参生长于海拔1 500~2 800米的山地、溪谷疏林中或山坡路边, 主要分布于我国云南、四川、贵州、湖南、广西和西藏等省区[2]。二者生境相似且分布区域有部分重叠。
由于昆明杯冠藤和青羊参形态相似且分布区域有部分重叠, 使得二者很难被区分, 因此, 在药材采收过程中容易发生鉴定错误, 引起混用或误用[5]。中药近缘物种的准确鉴定是安全用药的前提, 药材混用会威胁用药的安全性和影响疗效。这两个近缘物种容易被混淆的问题也曾得到部分学者的关注, 如Yang等[6, 7]曾先后使用生药学鉴别和随机扩增多态性DNA (RAPD) 技术对青羊参及其近缘种进行研究, 其结果为其物种鉴定提供了一定参考。
近年来, 由于测序技术的发展, 叶绿体基因组研究日益受到更多学者的重视[8, 9]。本研究比较分析了昆明杯冠藤和青羊参叶绿体基因组的基本特征和系统发育关系, 旨在为这两种中药材的安全用药提供依据和保证, 以及为其同属植物的种质资源鉴定、系统发育分析和资源利用保护等方面的研究提供基础数据。
材料与方法
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实验材料  昆明杯冠藤采自云南保山芒宽(25°5.114′N, 98°48.745′E), 青羊参采自云南丽江拉市海(26°52.330′N, 100°9.494′E), 经云南中医药大学杨从卫老师鉴定确认。凭证标本号分别为YUCM2021001和YUCM2022016, 存放于云南中医药大学。选取健康植株幼嫩叶片, 经液氮速冻后, 置超低温冰箱中保存备用。除昆明杯冠藤和青羊参叶绿体基因组外, 其余样本均从NCBI下载(表 1)。
DNA的提取和测序  使用改良的十六烷基三甲基溴化铵(CTAB) 方法提取昆明杯冠藤和青羊参的总DNA[10]。利用Illumina Novaseq6000高通量测序平台对青羊参和昆明杯冠藤进行双末端测序, 构建插入片段为350~450 bp的文库, reads长度为150 bp。另采用PacBio Sequel Ⅱ平台对昆明杯冠藤进行测序, 构建插入片段为20 kb的文库。使用Trimmomatic v0.39对原始数据进行数据过滤, 最终获得clean reads用于后续组装和注释流程[11]。
叶绿体基因组组装和注释  使用GetOrganelle v1.7.5对Illumina测序数据进行组装, 另使用BWA v0.7.17将昆明杯冠藤二代组装序列比对到Pacbio三代数据, 再使用SPAdes v3.14.1进行混合组装[12, 13]。利用在线工具GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) 对组装好的序列进行编码蛋白(PCGs)、转运RNA (tRNA) 和核糖体RNA (rRNA) 的预测, 得到原始注释结果。参考鹅绒藤属物种叶绿体基因组的注释信息, 在Geneious v2023.0.1[14]中对昆明杯冠藤和青羊参叶绿体基因组的注释信息进行检查及人工校正, 得到高准确性的基因集。通过BankIt将注释结果提交到NCBI, 获得昆明杯冠藤和青羊参叶绿体基因组的登录号: OQ198623和OQ928061。最后, 利用在线工具OGDRAW (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html) 绘制圈图。
叶绿体基因组特征分析  使用CodonW v1.4.2计算昆明杯冠藤和青羊参叶绿体基因组中蛋白编码序列的相对同义密码子使用度(relative synonymous codon usage, RSCU)[15]。结合在线工具CUSP (https://www.bioinformatics.nl/emboss-explorer/) 计算蛋白编码序列的总GC含量及密码子第1位、第2位和第3位的GC含量。蛋白编码基因的筛选标准为起始密码子为ATG, 并以TAA、TAG、TGA结尾; 序列长度≥ 300 bp; 且双拷贝基因只选取一个[16]。使用MISA软件[17]对叶绿体基因组序列进行简单重复序列(simple sequence repeats, SSRs) 分析, 单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸的最小重复值分别设置为10、5、4、3、3和3, 两个SSR之间的最小距离设置为100 bp。
叶绿体基因组比较分析  利用IRscope (https://irscope.shinyapps.io/irapp/) 对鹅绒藤属物种叶绿体基因组边界的收缩与扩张进行可视化。使用mVISTA[18]对昆明杯冠藤和青羊参在内的鹅绒藤属8种植物的叶绿体基因组进行比较分析, 选择Shuffle-LAGAN模式。通过DnaSP v6.12.03软件[19]计算鹅绒藤属物种叶绿体基因组共有基因和共有基因间区的核苷酸多态性(nucleotide diversity, Pi)。
DNA条形码鉴定分析  以共有间区序列中Pi值排名靠前的序列为模板设计引物, 并对包括昆明杯冠藤和青羊参在内的9份样本进行PCR实验验证(表 2)。筛选出rps16-trnQ-UUG序列可用于鉴定昆明杯冠藤和青羊参。rps16-trnQ-UUG序列的引物(F: 5ʹ-ATTG GTTTGTAGACATCGTA-3ʹ, R: 5ʹ-TAAAGTCTAATGT TAGCTGGA-3ʹ) 由上海生工生物工程有限公司合成。PCR扩增采用25 μL反应体系, 包括2×EasyTaq® PCR SuperMix (北京全式金生物技术有限公司) 12.5 μL, 上下游引物(2.5 μmol·L-1) 各1 μL, DNA模板2 μL, ddH2O 8.5 μL。扩增程序: 94 ℃预变性5 min; 94 ℃变性30 s, 52 ℃退火30 s, 72 ℃延伸45 s, 35个循环; 72 ℃终延伸10 min。使用ABI3730XL测序仪对扩增产物进行Sanger测序, 利用SeqMan软件[20]对序列进行拼接。使用MEGA X软件[21]进行序列比对并以Kimura 2-parameter (K2-P) 模型计算遗传距离。最后采用邻接法(neighbor joining, NJ) 构建系统发育树, 设置Bootstrap值为1 000。
系统发育分析  为探究昆明杯冠藤和青羊参的系统发育地位和亲缘关系, 从NCBI下载了24个夹竹桃科马利筋亚科(Asclepiadoideae) 植物样本的叶绿体基因组(表 1)。另将夹竹桃亚科(Apocynoideae) 的白麻(Apocynum pictum)、罗布麻(Apocynum venetum) 和夹竹桃(Nerium oleander) 的叶绿体基因组作为外类群, 与包括昆明杯冠藤和青羊参叶绿体基因组在内的共26个马利筋亚科植物样本一起构建系统发育树。通过MAFFT v7.490对叶绿体基因组全序列进行多重序列比对, 最后使用IQ-TREE基于最大似然法(Maximum likelihood, ML) 构建系统发育树, 进行1 000次重复的Bootstrap检验[22, 23]。
结果
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1 叶绿体基因组基本信息
昆明杯冠藤和青羊参分别获得8 234和5 069 Mb二代原始测序数据, 另昆明杯冠藤获得127.96 Mb三代原始测序数据。最终组装得到叶绿体基因组全长分别为159 808和161 050 bp, 均具有典型的双链环状四分体结构, 包括1个大单拷贝区(large single copy, LSC)、1个小单拷贝区(small single copy, SSC) 和1对反向重复区(inverted repeats, IR) (图 1)。昆明杯冠藤和青羊参叶绿体基因组LSC的长度分别为90 901和92 009 bp, SSC的长度分别为20 943和19 833 bp, IR的长度分别为23 982和24 604 bp (表 3)。昆明杯冠藤和青羊参叶绿体基因组序列的总GC含量分别为37.87%和37.79% (表 3), 其中IR区的GC含量分别为43.70%和43.21%, 均高于LSC区(36.15%、36.13%) 和SSC区(31.92%、32.01%)。IR区含有GC含量较高的4种rRNA, 这可能是引起IR区GC含量偏高的一个因素。
昆明杯冠藤和青羊参叶绿体基因组均注释得到133个基因, 有19个是双拷贝基因(表 4)。133个基因中包含88个PCGs、37个tRNAs和8个rRNAs。除tRNA和rRNA外, 88个蛋白编码基因根据功能不同分为4类: 45个与光合作用相关的基因, 包括5个光系统Ⅰ基因、15个光系统Ⅱ基因、12个NADH脱氢酶基因、6个细胞色素b/f复合物编码基因、6个ATP合成酶基因和1个Rubisco大亚基基因; 29个与遗传复制系统相关的基因, 包括11个核糖体大亚基基因、14个核糖体小亚基基因和4个RNA聚合酶基因; 此外, 还有8个功能未知基因和6个其他基因。叶绿体基因组中4种rRNA (rrn4.5S, rrn5S, rrn16S, rrn23S) 均位于IR区, 存在双拷贝。在37个tRNA中, trnA-UGC、trnI-CAU、trnI-GAU、trnL-CAA、trnN-GUU、trnR-ACG和trnV-GAC等7个基因是双拷贝基因。
2 叶绿体基因组密码子使用偏好性分析
从昆明杯冠藤和青羊参叶绿体基因组中均筛选出53条蛋白编码序列, 基于这部分序列分析两个物种的密码子使用偏好性。在两者蛋白编码序列中, 分别有21 248和21 119个密码子, 除终止密码子外, 均编码20种氨基酸(图 2)。除甲硫氨酸(Met)和色氨酸(Trp) 外, 其他氨基酸都有多个同义密码子。其中精氨酸(Arg)、亮氨酸(Leu) 和丝氨酸(Ser) 有6个同义密码子; 丙氨酸(Ala)、甘氨酸(Gly)、脯氨酸(Pro)、苏氨酸(Thr) 和缬氨酸(Val) 均有4个同义密码子; 异亮氨酸(Ile) 有3个同义密码子; 其余9个氨基酸有2个同义密码子。如图 2所示, 昆明杯冠藤和青羊参叶绿体基因组中密码子数量最多的都是Leu, 分别占总密码子的10.44%和10.41%; 其次为Ile, 分别占8.08%和8.20%; 编码半胱氨酸(Cys) 的密码子数量最少, 分别占1.16%和1.14%。此外, 昆明杯冠藤和青羊参叶绿体基因组中均有30种密码子的RSCU大于1, 对应密码子在编码过程中具有偏好性, 其中RSCU最大的均是编码Leu的UUA。编码Met和Trp的密码子分别为AUG和UGG, 两者RSCU等于1, 表示在编码过程中没有使用偏好。其余密码子的RSCU小于1, 这些密码子的使用率较低, 其中RSCU最小的密码子均为编码Leu的CUC。
经统计, 昆明杯冠藤和青羊参叶绿体基因组中编码氨基酸的密码子的总GC含量均为38.62%, 仅第3位的GC含量分别为30.57%和30.50%。表明两个物种叶绿体基因组中密码子使用偏好A/U, 且在密码子第3位有强烈的A/U偏好性。
3 简单重复序列SSR分析
从昆明杯冠藤和青羊参叶绿体基因组中分别检测到91个和103个SSR, 均检测到了6种类型的微卫星序列。在昆明杯冠藤叶绿体基因组中发现了61个单核苷酸、9个二核苷酸、4个三核苷酸、12个四核苷酸、1个五核苷酸和4个六核苷酸。在青羊参叶绿体基因组中发现了63个单核苷酸、10个二核苷酸、7个三核苷酸、16个四核苷酸、2个五核苷酸和5个六核苷酸。如图 3所示, 在6种类型的微卫星序列中, 大多为单碱基重复型微卫星序列, 其中以A/T类型重复占比最大, 分别占64.8%和60.2%, 重复单元数目的范围为10~18。三核苷酸、五核苷酸及六核苷酸重复序列出现频率较低。
4 叶绿体全基因组边界特征分析
比较分析昆明杯冠藤和青羊参叶绿体基因组与鹅绒藤属其他物种在进化过程中边界的扩张与收缩情况。如图 4所示, 8个物种的边界具有保守性, 边界处基因基本相同, 但其存在一定的扩张与收缩现象。其中LSC/IRb边界(JLB) 和LSC/IRa边界(JLA) 的侧翼基因完全相同。在JLB边界, 均为rps19基因(位于LSC区) 和rpl2基因(位于IRb区), rps19基因末端到JLB边界的距离为4~14 bp。在JLA边界, 均为trnH-GUG基因(位于LSC区) 和rpl2基因(位于IRa区), trnH-GUG基因末端到JLA边界的距离为1~7 bp。SSC/IRb边界(JSB) 显示, 鹅绒藤属植物JSB边界的基因为ycf1假基因和ndhF基因(位于SSC区), 其中青羊参、隔山消(Cynanchum wilfordii)、白首乌(Cynanchum bungei) 和牛皮消(Cynanchum auriculatum) 叶绿体基因组的JSB边界位于ycf1假基因内; 地梢瓜(Cynanchum thesioides)、鹅绒藤(Cynanchum chinense) 和戟叶鹅绒藤(Cynanchum sibiricum) 中ycf1假基因位于JSB边界左翼; 而昆明杯冠藤中ycf1假基因位于JSB边界右翼, 距离JSB边界166 bp。SSC/IRa边界(JSA) 显示, 青羊参、隔山消、牛皮消和鹅绒藤的JSA边界均位于ycf1基因内; 昆明杯冠藤和白首乌的JSA边界位于ycf1基因右翼; 戟叶鹅绒藤的JSA边界位于ycf1基因左翼。
5 叶绿体基因组序列变异分析
为了解鹅绒藤属植物叶绿体基因组序列的差异程度, 采用mVISTA在线工具, 以牛皮消作为参考序列, 对昆明杯冠藤、青羊参、牛皮消、鹅绒藤、白首乌、地梢瓜、隔山消和戟叶鹅绒藤等鹅绒藤属物种的叶绿体基因组进行全序列比对的可视化分析。结果显示(图 5), 鹅绒藤属植物种间叶绿体基因组编码基因的类别及基因排列顺序均高度一致。分析发现, 鹅绒藤属植物叶绿体基因组变异较高的区域主要集中在LSC区和SSC区, 其中SSC区域的变异程度最高, 且序列中非编码区域的变异高于编码区域。相较LSC和SSC区而言, IR区具有较高的保守性, 变异程度最低, 编码基因中tRNA和rRNA的序列基本无差异。
6 核苷酸多态性分析
从鹅绒藤属物种叶绿体基因组序列中分别提取共有基因和共有间区序列, 经MAFFT比对后, 使用DnaSP v6.12.03软件[19]计算核苷酸多态性值。结果显示(图 6), 共有间区序列的Pi值普遍高于共有基因序列, 这与mVISTA分析结果一致。在共有间区序列中, trnH-GUG-psbA、trnQ-UUG-psbK、ccsA-ndhD、rps16-trnQ-UUG、rpl32-trnL-UAG、ndhC-trnV-UAC、trnE-UUC-trnT-GGU、rps4-trnT-UGU、trnP-UGG-psaJ、petN-psbM、trnT-UGU-trnL-UAA和trnS-UGA-psbZ等12个间区序列的Pi值均大于0.040。在共有基因序列中, rps19、rpl20、rpl16、rpl32、rps16、rpl22、rps18、ndhA、rps15、rps3、rpoA、trnK_UUU、rps11、trnG_UCC、petD、ndhD和psbK等17个共有基因序列的Pi值均大于0.015。
7 基于叶绿体基因组高变区的DNA条形码鉴定及分析
遗传距离显示, rps16-trnQ-UUG序列对应的昆明杯冠藤和青羊参的种内遗传距离均为0, 牛皮消种内遗传距离为0~0.002 0。昆明杯冠藤与青羊参的种间遗传距离为0.021 1~0.022 9, 昆明杯冠藤与牛皮消的种间遗传距离为0.027 8~0.028 8, 牛皮消与青羊参种间遗传距离为0.015 6~0.016 2。各样品序列的最大种内遗传距离均小于最小种间遗传距离, 不存在重叠, 说明所筛选片段符合DNA条形码的要求。NJ系统树结果也表明, 三个物种各自形成独立的分支(图 7)。因此, rps16-trnQ-UUG可以作为特异性DNA条形码用于昆明杯冠藤和青羊参的鉴定。
8 系统发育分析
为了解昆明杯冠藤和青羊参的系统发育地位, 以夹竹桃亚科的白麻、罗布麻和夹竹桃作为外类群, 选取昆明杯冠藤和青羊参在内的共26个马利筋亚科物种的叶绿体基因组序列一起构建系统发育树。除昆明杯冠藤和青羊参外, 其余样本数据均从NCBI下载(表 1)。系统发育树显示(图 8), 所有的分支均具有较高的支持率(> 80%), 说明结果可靠, 鹅绒藤属10个样本均以100%的支持率聚为一支。除外类群外, 26个样本聚为两大类, 分别为马利筋族(Asclepiadeae) 和牛奶菜族(Marsdenieae)。在鹅绒藤属分支中, 昆明杯冠藤和地梢瓜聚在一起, 两者亲缘关系较近; 青羊参、白首乌和隔山消三者亲缘关系较近, 聚为一支, 且进一步与牛皮消形成姐妹支。
讨论
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叶绿体是绿色植物进行光合作用的场所, 具有独立基因组[24]。与线粒体基因组或细胞核基因组相比, 叶绿体基因组在进化过程中具有高度的保守性和稳定性, 在物种鉴定、系统发育、DNA条形码开发及遗传工程研究等领域运用广泛[25]。目前, 有学者根据物种间叶绿体基因组的特征分析和系统发育关系来研究同属近缘物种[26-28]。昆明杯冠藤和青羊参形态特征相似且分布地区有部分重叠, 使两者鉴别难度增加, 且药材混用会对消费者的安全造成威胁[2, 29, 30]。因此, 有必要为昆明杯冠藤和青羊参的鉴定提供更多可靠的证据。
和其他被子植物一样, 昆明杯冠藤和青羊参叶绿体基因组呈典型的四分体结构, 两者编码基因的数量、类别和排列顺序一致[31]。IR区的扩张和收缩被认为是造成叶绿体基因组差异性的主要原因[32]。分析发现, 鹅绒藤属物种的IR区的长度范围为23 982 ~24 689 bp, 有不同程度的扩张或收缩, 导致种间叶绿体基因组各区域的长度和边界处基因存在差异, 特别是SSC区与IR区边界处的基因差异较明显。昆明杯冠藤和青羊参叶绿体基因组的密码子偏好性与豆蔻属、刺柏属等植物相似, 密码子使用偏好A/U[16, 33]。从昆明杯冠藤和青羊参叶绿体基因组序列中分别检测到91个和103个SSR, 两者均具有丰富的基元类型, 与其他被子植物SSR特点一致[26, 34, 35], 均以A/T类型占比最大。这些SSR广泛分布于叶绿体基因组的不同位置, 可为物种的分子标记提供参考。鹅绒藤属叶绿体全基因组序列的变异分析发现, 其具有高度相似性, 相较LSC区和SSC区而言, IR区变异程度最低。此外, 鹅绒藤属叶绿体基因组中非编码区的变异普遍高于编码区, 与丝兰属、苍术属和胡桃科等一致[27, 36, 37]。其中trnH-GUG-psbA、trnQ-UUG-psbK、ccsA-ndhD、rps16-trnQ-UUG、rps19、rpl20、rpl16、rpl32等Pi值较高的共有间区和共有基因, 可为鹅绒藤属的物种鉴定和系统进化分析提供参考。本研究筛选出rps16-trnQ-UUG可作为特异性DNA条形码用于昆明杯冠藤和青羊参的快速、准确鉴定。
鹅绒藤属植物因性状相似, 形态界限模糊, 一直是分类学争议不休的类群[38]。有学者曾先后使用生药学鉴别手段和RAPD技术对青羊参及其近缘种进行了研究, 但生药学鉴别需要研究人员具备丰富的生药学鉴定知识和长期的经验积累且传统的性状特征和显微组织结构不易区分, 而RAPD技术重复性差、可靠性低, 均限制了其广泛应用[6, 7, 39]。近年来, 随着分子生物学技术的发展, 分子鉴定技术在中药学领域逐渐得到推广[39, 40]。Guo等[41]研究涉及到了昆明杯冠藤和青羊参两个物种, 但因分子标记少, 序列较短, 未能明确解决昆明杯冠藤和青羊参二者的系统关系。作为一个药用价值丰富的类群, 进一步界定昆明杯冠藤和青羊参的系统位置十分必要。本研究表明, 鹅绒藤属样本单独聚在一个分支上, 与Chen等[42, 43]的研究结果一致。在鹅绒藤属分支上, 昆明杯冠藤和青羊参分别与同属其他物种各自形成单系, 表明二者虽然形态相似但在遗传上并不具有最近的亲缘关系。药用植物亲缘关系越相近, 化学成分越相似[44, 45]。两者在叶绿体基因组水平上并不位于同一单系中, 其化学成分必然有所区别, 功效和用途上具有差异, 因此, 在用药前应确保物种鉴定无误且不能混用。
本研究首次完成了昆明杯冠藤和青羊参叶绿体基因组的比较研究, 将二者与已报道的鹅绒藤属其他物种的叶绿体基因组进行对比分析。该研究不仅丰富了夹竹桃科植物的遗传资源, 也从分子水平上为鉴别鹅绒藤属近缘物种提供了基础, 为昆明杯冠藤和青羊参的遗传多样性研究和资源保护提供了参考。
作者贡献: 耿应敏负责实验、数据分析、论文写作及修改; 周兴乾参与部分数据分析; 张体操参与论文修改; 郑兰平负责论文设计、样品收集、实验、数据分析及论文修改。
利益冲突: 所有作者均声明不存在任何利益冲突。
基金
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  • 云南省基础研究项目(202301AT070254)
  • 云南省应用基础研究中医联合专项(202101AZ070001-056)
文献
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参考文献 引证文献
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2024年第59卷第3期
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doi: 10.16438/j.0513-4870.2023-0691
  • 接收时间：2023-05-31
  • 首发时间：2025-11-28
  • 出版时间：2024-03-12
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  • 收稿日期：2023-05-31
  • 修回日期：2023-07-21
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云南省基础研究项目(202301AT070254)
云南省应用基础研究中医联合专项(202101AZ070001-056)
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    云南中医药大学中药学院, 云南 昆明 650500

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*郑兰平, 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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