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Article(id=1308842640502784842, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308842471539442166, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2026-0239, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1772640000000, receivedDateStr=2026-03-05, revisedDate=1778515200000, revisedDateStr=2026-05-12, acceptedDate=null, acceptedDateStr=null, onlineDate=1789982002616, onlineDateStr=2026-09-21, pubDate=1786464000000, pubDateStr=2026-08-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1789982002616, onlineIssueDateStr=2026-09-21, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1789982002616, creator=13701087609, updateTime=1789982002616, updator=13701087609, issue=Issue{id=1308842471539442166, tenantId=1146029695717560320, journalId=1189982191388893191, year='2026', volume='61', issue='8', pageStart='2821', pageEnd='3220', issueExtLink='null', onlineDate='null', pubDate='1786464000000', pubDateStr='2026-08-12', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1789981962332, creator='13701087609', updateTime=1789984137222, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1308851593773150481, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308842471539442166, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1308851593773150482, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1308842471539442166, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=3186, endPage=3198, ext={EN=ArticleExt(id=1308842640699917131, articleId=1308842640502784842, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Characteristics and phylogenetic analysis of the chloroplast genome of Oplopanax elatus Nakai, columnId=1190335348761793317, journalTitle=Acta Pharmaceutica Sinica, columnName=Original Articles, runingTitle=null, highlight=null, articleAbstract=

Oplopanax elatus Nakai is a deciduous shrub within the Araliaceae family and is classified as a first-class protected plant in Jilin Province. To elucidate the structural characteristics of its chloroplast genome and phylogenetic relationships, this study conducted chloroplast genome sequencing of one cultivated individual and five wild populations of O. elatus, followed by comparative chloroplast genomic and phylogenetic analyses with published congeneric species of Oplopanax and allied genera of Araliaceae deposited in GenBank. The results revealed that the chloroplast genomes of the six O. elatus accessions ranged from 156 108-156 193 bp in length, with a uniform GC content of 38.03%. A total of 129-133 genes were annotated, comprising 87-88 protein-coding genes, 6-8 rRNA genes, and 36-37 tRNA genes. The chloroplast genome of cultivated O. elatus contained one additional protein-coding gene compared to those of wild accessions. Using the chloroplast genome sequence of cultivated O. elatus as reference, sequence alignment against wild populations identified 36 single nucleotide polymorphism (SNP) loci and 10 insertion-deletion (InDel) loci. SNPs were distributed in both intergenic spacers and coding sequences (CDS), whereas all InDels were restricted to the large single-copy (LSC) region. Nucleotide diversity (Pi) analysis of the 13 chloroplast genomes detected two hypervariable regions, clpP1-exon3_clpP1-exon2 and ycf1, which are proposed as candidate DNA barcodes and molecular markers for O. elatus. Analysis of codon preference indicated that all 13 samples exhibited a preference for codons terminating in A or T. Discrepancies in codon numbers were observed between cultivated and wild O. elatus chloroplast genomes. A total of 545 simple sequence repeat (SSR) loci and 498 dispersed repeat sequences were identified within the 13 chloroplast genomes. Phylogenetic reconstruction based on branch support values and clustering patterns partitioned the eight Araliaceae genera into four clades. The genus Oplopanax formed a highly supported monophyletic lineage positioned centrally within the tree, diverging subsequently to Panax and constituting a sister group to the fourth major clade, with its closest affinity to Schefflera. This investigation advances the understanding of evolutionary dynamics within Oplopanax and allied genera, with the acquired genomic resources providing a foundation for DNA barcode screening and germplasm conservation of the genus.

, authors=Guang-yi XIANG, Hong-juan TANG, Hui-fang LI, Han-bing LI, Lin CHENG, Yong-gang ZHANG*, authorsList=Guang-yi XIANG, Hong-juan TANG, Hui-fang LI, Han-bing LI, Lin CHENG, Yong-gang ZHANG, authorCompany=null, correspAuthors=Yong-gang ZHANG, 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=1308842644088914782, articleId=1308842640502784842, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=刺参叶绿体基因组特征与系统发育分析, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

刺参(Oplopanax elatus Nakai) 为五加科刺参属落叶灌木, 是吉林省一级保护植物。为明确其叶绿体基因组结构特征及系统发育关系, 本研究对1个栽培刺参和5个野生刺参居群个体进行叶绿体基因组测序, 并与已在GenBank上发表的刺参属和五加科近缘属物种进行叶绿体基因组比较和系统进化分析。结果表明: 6个居群刺参叶绿体基因组大小为156 108~156 193 bp, GC含量均为38.03%, 共注释到129~133个基因, 其中蛋白编码基因为87或88个, rRNA基因为6~8个, tRNA基因为36或37个。栽培刺参比野生刺参叶绿体基因组均多一个蛋白编码基因。以栽培刺参叶绿体基因组序列为参考, 与野生居群刺参进行序列比对, 共检测到36个SNP (single nucleotide polymorphism) 位点和10个InDel (insertion-deletion) 位点, SNP位点在基因间区和CDS区(coding sequences) 均有分布, 而InDel位点则全部分布于LSC区(large single-copy)。在13个样本叶绿体基因组的核苷酸多态性分析中检测到clpP1-exon3_clpP1-exon2、ycf1两个高多态区段, 可作为刺参DNA条形码候选区及分子标记开发。密码子偏好性分析揭示, 13个样本密码子偏好使用以A或T结尾的密码子。栽培与野生刺参叶绿体基因组在密码子数量方面存在差异。13个样本叶绿体基因组中检测到545个简单重复序列位点和498条散在重复序列。根据系统发育树各分支的支持率及聚类情况, 可将五加科8个属物种划分为四个分支, 刺参属以高支持率独立成支, 位于该树的中间位置, 分化时间比人参属晚, 与第四大分支互为姐妹群, 与鹅掌柴属亲缘关系最近。本研究增进了对刺参属及其近缘属进化的认识, 所获得遗传资源将为刺参属DNA条形码筛选、种质资源保护提供基因组学依据。

, authors=向光亿, 唐红鹃, 李慧芳, 李涵冰, 程林, 张永刚*, authorsList=向光亿, 唐红鹃, 李慧芳, 李涵冰, 程林, 张永刚, authorCompany=null, correspAuthors=张永刚, authorNote=

作者贡献:

向光亿为本文的第一作者, 负责数据分析、文章撰写、稿件修改; 唐红鹃和李涵冰负责材料的处理, 李慧芳和程林负责样品采集; 张永刚为本文的通讯作者, 负责实验设计及论文审阅。

, correspAuthorsNote=
张永刚, E-mail:
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New insights into phylogenetic relationship of Hydrocotyle (Araliaceae) based on plastid genomes [J]. Int J Mol Sci, 2023, 24: 16629., articleTitle=null, refAbstract=null), Reference(id=1308842656986399700, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=47, rfOrder=46, authorNames=null, journalName=null, refType=null, unstructuredReference=Li R, Wen J. Phylogeny and diversification of Chinese Araliaceae based on nuclear and plastid DNA sequence data [J]. J Syst Evol, 2016, 54: 453-467., articleTitle=null, refAbstract=null)], funds=null, companyList=[AuthorCompany(id=1308842644332184415, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, xref=null, ext=[AuthorCompanyExt(id=1308842644344767328, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, companyId=1308842644332184415, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China), AuthorCompanyExt(id=1308842644353155937, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, companyId=1308842644332184415, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=吉林农业大学中药材学院, 吉林 长春 130118)])], figs=[ArticleFig(id=1308842648279024524, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=pgK08ODhMT1uOEqhhpnz1g==, figureFileBig=JwOp7Va3dnZluXcXCXof2A==, tableContent=null), ArticleFig(id=1308842648346133389, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.1, caption=Chloroplast genome map of O. elatus. The outer circle shows the positional coordinates of genomic components such as genes and ncRNAs. The inner circle shows the genomic GC content. LSC: Large single-copy; SSC: Small single-copy; IRa: Inverted repeat a; IRb: Inverted repeat b, figureFileSmall=pgK08ODhMT1uOEqhhpnz1g==, figureFileBig=JwOp7Va3dnZluXcXCXof2A==, tableContent=null), ArticleFig(id=1308842648555848590, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=ukVGEH7luUU13oVg+cOcZw==, figureFileBig=fp7qWcsd5nVB+zajzt0Xew==, tableContent=null), ArticleFig(id=1308842648627151759, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.2, caption=Analysis of simple sequence repeats in the chloroplast genomes of 13 Araliaceae samples. A: Total number of SSRs detected in each chloroplast genome and their different types; B: The number of SSR repeats in the IRa, IRb, LSC, and SSC regions of the chloroplast genome of each sample. SSR: Simple sequence repeat, figureFileSmall=ukVGEH7luUU13oVg+cOcZw==, figureFileBig=fp7qWcsd5nVB+zajzt0Xew==, tableContent=null), ArticleFig(id=1308842648702649232, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=IY4YZqpAEusrM5y7bSX3Lw==, figureFileBig=zkKotwRUr3qRd6wCRhKjnA==, tableContent=null), ArticleFig(id=1308842648773952401, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.3, caption=Analysis of scattered repeats sequences in the chloroplast genomes of 13 samples of the Araliaceae. A: Types and numbers of scattered repeats in the chloroplast genome; B: The number of scattered repeats longer than 30 bp in each chloroplast genome, figureFileSmall=IY4YZqpAEusrM5y7bSX3Lw==, figureFileBig=zkKotwRUr3qRd6wCRhKjnA==, tableContent=null), ArticleFig(id=1308842648853644178, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=DuUcCtz1uiWbttJzOLKkKQ==, figureFileBig=rkDL8eOVSxfUrsdaOsiBRA==, tableContent=null), ArticleFig(id=1308842648924947347, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.4, caption=Heat map of relative synonymous codon use values in 13 intact chloroplast genomes of the Araliaceae family. Red indicates a higher RSCU value and blue indicates a lower RSCU value, figureFileSmall=DuUcCtz1uiWbttJzOLKkKQ==, figureFileBig=rkDL8eOVSxfUrsdaOsiBRA==, tableContent=null), ArticleFig(id=1308842649013027732, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=MUBv4BpQrPNKTUtK/aaapg==, figureFileBig=hnCKb2iCaxT15Pk1/MTdiw==, tableContent=null), ArticleFig(id=1308842649092719509, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.5, caption=Comparison of the complete chloroplast genome sequences of 13 Araliaceae species. The first one is the reference genome, and different colors represent different regions. The horizontal axis indicates the coordinates within the chloroplast genome. The vertical scale shows the identity percentage, ranging from 50% to 100%., figureFileSmall=MUBv4BpQrPNKTUtK/aaapg==, figureFileBig=hnCKb2iCaxT15Pk1/MTdiw==, tableContent=null), ArticleFig(id=1308842649164022678, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=jfHCIC/PEIlsUVCbu8Nd3g==, figureFileBig=ejCq7K3uWPCXooNeobJrKQ==, tableContent=null), ArticleFig(id=1308842649243714455, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.6, caption=Contraction and expansion of IR boundaries in 13 genomes of the Araliaceae family. Each horizontal rectangle represents a genome, with the topmost one being the reference genome. Different colors denote distinct regions. Numbers indicate the distance from genes to IR boundaries. JLB: LSC-IRb; JSB: IRb-SSC; JSA: SSC-IRa; JLA: IRa-LSC, figureFileSmall=jfHCIC/PEIlsUVCbu8Nd3g==, figureFileBig=ejCq7K3uWPCXooNeobJrKQ==, tableContent=null), ArticleFig(id=1308842649335989144, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=reIkZtOWjUu1ixKiGtViaw==, figureFileBig=OHH5zm4lMSo+mPjQLquPnA==, tableContent=null), ArticleFig(id=1308842649440846745, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.7, caption=Pi value distribution curves of 13 chloroplast genomes in the Araliaceae family. The horizontal axis represents genome coordinates, and the vertical axis represents Pi values. The red dashed line indicates the threshold boundary, with regions above this line identified as genomic variation hotspots, figureFileSmall=reIkZtOWjUu1ixKiGtViaw==, figureFileBig=OHH5zm4lMSo+mPjQLquPnA==, tableContent=null), ArticleFig(id=1308842649507955610, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=xQJuZffFg9K4T8PxMVAlYA==, figureFileBig=82gIO9g6ZdNslnd8mfEk0w==, tableContent=null), ArticleFig(id=1308842649566675867, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.8, caption=Pairwise Ka/Ks values of 13 samples from the Araliaceae family. Color scale indicates Ka/Ks values, with blue representing purifying selection (Ka/Ks < 1) and red indicating positive selection (Ka/Ks > 1), figureFileSmall=xQJuZffFg9K4T8PxMVAlYA==, figureFileBig=82gIO9g6ZdNslnd8mfEk0w==, tableContent=null), ArticleFig(id=1308842651261174684, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=vKW+FbxIb/Y+Ii1J0uuitw==, figureFileBig=Y3lQFQWc68UD3XPkZk6tFA==, tableContent=null), ArticleFig(id=1308842651332477853, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Fig.9, caption=Phylogenetic tree of 34 species constructed using the maximum likelihood method based on the complete chloroplast genome sequences. 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LocalityPopulationLongitudeLatitudeAltitude/mHabitat type
Dahuangou Village, Tonghua County, Jilin Provincecs-01125°40′45″42°13′57.32″308Mixed broadleaf-conifer forest
Baijifeng National Forest Park, Tonghua County, Jilin ProvinceBJF126°06′48.30″41°33′02.88″1 259Mixed broadleaf-conifer forest
Banjiegou, Baishan City, Jilin ProvinceBJG126°26′36.37″41°35′38.43″686Mixed broadleaf-conifer forest
Funan Forest Farm, Baishan City, Jilin ProvinceFN127°46′09.47″41°46′41.46″1 202Mixed broadleaf-conifer forest
Xiaodongshan Forest Farm, Baishan City, Jilin ProvinceXDS1127°45′53.45″41°42′47″1 518Mixed broadleaf-conifer forest
Guanmenshan National Forest Park, Benxi City, Liaoning ProvinceGMS124°05′42.56″41°07′48.20″906Mixed broadleaf-conifer forest
), ArticleFig(id=1308842651466695583, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Tab.1, caption=

O. elatus sample collection information

, figureFileSmall=null, figureFileBig=null, tableContent=
LocalityPopulationLongitudeLatitudeAltitude/mHabitat type
Dahuangou Village, Tonghua County, Jilin Provincecs-01125°40′45″42°13′57.32″308Mixed broadleaf-conifer forest
Baijifeng National Forest Park, Tonghua County, Jilin ProvinceBJF126°06′48.30″41°33′02.88″1 259Mixed broadleaf-conifer forest
Banjiegou, Baishan City, Jilin ProvinceBJG126°26′36.37″41°35′38.43″686Mixed broadleaf-conifer forest
Funan Forest Farm, Baishan City, Jilin ProvinceFN127°46′09.47″41°46′41.46″1 202Mixed broadleaf-conifer forest
Xiaodongshan Forest Farm, Baishan City, Jilin ProvinceXDS1127°45′53.45″41°42′47″1 518Mixed broadleaf-conifer forest
Guanmenshan National Forest Park, Benxi City, Liaoning ProvinceGMS124°05′42.56″41°07′48.20″906Mixed broadleaf-conifer forest
), ArticleFig(id=1308842651554775968, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesFamilyGenusAccession
Oplopanax japonicusAraliaceaeOplopanaxNC_082542
Oplopanax elatusAraliaceaeOplopanaxNC_085753
Oplopanax japonicus var. japonicusAraliaceaeOplopanaxOR 346900
Oplopanax japonicus var. japonicusAraliaceaeOplopanaxOR 346905
Oplopanax horridusAraliaceaeOplopanaxMK943805
Eleutherococcus brachypusAraliaceaeEleutherococcusNC_050832
Eleutherococcus senticoscusAraliaceaeEleutherococcusNC_016430
Eleutherococcus leucorrhizus var. sethchuenensisAraliaceaeEleutherococcusNC_062722
Eleutherococcus gracilistylusAraliaceaeEleutherococcusNC_062721
Eleutherococcus giraldiiAraliaceaeEleutherococcusNC_062723
Eleutherococcus eleutheristylusAraliaceaeEleutherococcusNC_062720
Brassaiopsis angustifoliaAraliaceaeBrassaiopsisNC_065370
Brassaiopsis hainlaAraliaceaeBrassaiopsisNC_022811
Brassaiopsis tripterisAraliaceaeBrassaiopsisNC_088755
Aralia continentalisAraliaceaeAraliaNC_041648
Aralia atropurpureaAraliaceaeAraliaNC_056999
Aralia cordataAraliaceaeAraliaNC_040964
Dendropanax oligodontusAraliaceaeDendropanaxNC_053618
Dendropanax morbiferAraliaceaeDendropanaxNC_027607
Schefflera actinophyllaAraliaceaeScheffleraNC_049889
Schefflera heptaphyllaAraliaceaeScheffleraNC_029764
Panax ginsengAraliaceaePanaxKF431956
Panax quinquefoliusAraliaceaePanaxKT028714
Panax japonicusAraliaceaePanaxMK308678
Hydrocotyle sibthorpioidesAraliaceaeHydrocotyleNC_035502
Hydrocotyle verticillataAraliaceaeHydrocotyleNC_015818
Hydrocotyle sibthorpioides var. batrachiumAraliaceaeHydrocotyleNC_082588
Saposhnikovia divaricataApiaceaeSaposhnikoviaMW900177
Dendropanax morbiferAraliaceaeDendropanaxNC_027607
), ArticleFig(id=1308842651621884833, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=CN, label=Tab.2, caption=

Reference chloroplast genome information

, figureFileSmall=null, figureFileBig=null, tableContent=
SpeciesFamilyGenusAccession
Oplopanax japonicusAraliaceaeOplopanaxNC_082542
Oplopanax elatusAraliaceaeOplopanaxNC_085753
Oplopanax japonicus var. japonicusAraliaceaeOplopanaxOR 346900
Oplopanax japonicus var. japonicusAraliaceaeOplopanaxOR 346905
Oplopanax horridusAraliaceaeOplopanaxMK943805
Eleutherococcus brachypusAraliaceaeEleutherococcusNC_050832
Eleutherococcus senticoscusAraliaceaeEleutherococcusNC_016430
Eleutherococcus leucorrhizus var. sethchuenensisAraliaceaeEleutherococcusNC_062722
Eleutherococcus gracilistylusAraliaceaeEleutherococcusNC_062721
Eleutherococcus giraldiiAraliaceaeEleutherococcusNC_062723
Eleutherococcus eleutheristylusAraliaceaeEleutherococcusNC_062720
Brassaiopsis angustifoliaAraliaceaeBrassaiopsisNC_065370
Brassaiopsis hainlaAraliaceaeBrassaiopsisNC_022811
Brassaiopsis tripterisAraliaceaeBrassaiopsisNC_088755
Aralia continentalisAraliaceaeAraliaNC_041648
Aralia atropurpureaAraliaceaeAraliaNC_056999
Aralia cordataAraliaceaeAraliaNC_040964
Dendropanax oligodontusAraliaceaeDendropanaxNC_053618
Dendropanax morbiferAraliaceaeDendropanaxNC_027607
Schefflera actinophyllaAraliaceaeScheffleraNC_049889
Schefflera heptaphyllaAraliaceaeScheffleraNC_029764
Panax ginsengAraliaceaePanaxKF431956
Panax quinquefoliusAraliaceaePanaxKT028714
Panax japonicusAraliaceaePanaxMK308678
Hydrocotyle sibthorpioidesAraliaceaeHydrocotyleNC_035502
Hydrocotyle verticillataAraliaceaeHydrocotyleNC_015818
Hydrocotyle sibthorpioides var. batrachiumAraliaceaeHydrocotyleNC_082588
Saposhnikovia divaricataApiaceaeSaposhnikoviaMW900177
Dendropanax morbiferAraliaceaeDendropanaxNC_027607
), ArticleFig(id=1308842651693188002, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1308842640502784842, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Genome characteristicsO. elatus-cs01O. elatus-BJGO. elatus-FNO. elatus-XDS1O. elatus-BJFO. elatus-GMS
AccessionPX970985PX970987PX970989PX970988PX970986PX970990
Genome size/bp156 109156 193156 108156 109156 111156 109
LSC length/bp86 23686 31986 23586 23686 23986 237
SSC length/bp18 11118 11218 11118 11118 11218 112
IR length/bp25 88125 88125 88125 88125 88025 880
Total GC content/%38.0338.0338.0338.0338.0338.03
LSC GC content/%36.2436.2536.2436.2436.2436.24
SSC GC content/%32.1132.0932.1132.1132.0932.09
IR GC content/%43.0843.0843.0843.0843.0843.08
Total genes133132132132129132
Protein-coding genes888787878787
tRNA genes373737373637
rRNA genes888868
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Characteristics of chloroplast genomes of O. elatus. GC: Guanine-cytosine; tRNA: Transfer RNA; rRNA: Ribosomal RNA

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Genome characteristicsO. elatus-cs01O. elatus-BJGO. elatus-FNO. elatus-XDS1O. elatus-BJFO. elatus-GMS
AccessionPX970985PX970987PX970989PX970988PX970986PX970990
Genome size/bp156 109156 193156 108156 109156 111156 109
LSC length/bp86 23686 31986 23586 23686 23986 237
SSC length/bp18 11118 11218 11118 11118 11218 112
IR length/bp25 88125 88125 88125 88125 88025 880
Total GC content/%38.0338.0338.0338.0338.0338.03
LSC GC content/%36.2436.2536.2436.2436.2436.24
SSC GC content/%32.1132.0932.1132.1132.0932.09
IR GC content/%43.0843.0843.0843.0843.0843.08
Total genes133132132132129132
Protein-coding genes888787878787
tRNA genes373737373637
rRNA genes888868
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SampleTotal SNPCDS SNPIntergenic SNPTotal InDelCDS InDelInsertionDeletion
BJF11382011
BJG11384022
FN3031001
GMS11381001
XDS10002011
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SNP and InDel site information. SNP: Single nucleotide polymorphism; InDel: Insertion-deletion; CDS: Coding sequence

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SampleTotal SNPCDS SNPIntergenic SNPTotal InDelCDS InDelInsertionDeletion
BJF11382011
BJG11384022
FN3031001
GMS11381001
XDS10002011
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刺参叶绿体基因组特征与系统发育分析
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向光亿 , 唐红鹃 , 李慧芳 , 李涵冰 , 程林 , 张永刚 *
药学学报 | 研究论文 2026,61(8): 3186-3198
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药学学报 |研究论文 2026 , 61 (8) : 3186 -3198
刺参叶绿体基因组特征与系统发育分析
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向光亿, 唐红鹃, 李慧芳, 李涵冰, 程林, 张永刚*
作者信息
  • 吉林农业大学中药材学院, 吉林 长春 130118
通讯作者:
张永刚, E-mail:
作者简介:

作者贡献:

向光亿为本文的第一作者, 负责数据分析、文章撰写、稿件修改; 唐红鹃和李涵冰负责材料的处理, 李慧芳和程林负责样品采集; 张永刚为本文的通讯作者, 负责实验设计及论文审阅。

Characteristics and phylogenetic analysis of the chloroplast genome of Oplopanax elatus Nakai
Guang-yi XIANG, Hong-juan TANG, Hui-fang LI, Han-bing LI, Lin CHENG, Yong-gang ZHANG*
Affiliations
  • College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
出版时间: 2026-08-12 doi: 10.16438/j.0513-4870.2026-0239
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摘要
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刺参(Oplopanax elatus Nakai) 为五加科刺参属落叶灌木, 是吉林省一级保护植物。为明确其叶绿体基因组结构特征及系统发育关系, 本研究对1个栽培刺参和5个野生刺参居群个体进行叶绿体基因组测序, 并与已在GenBank上发表的刺参属和五加科近缘属物种进行叶绿体基因组比较和系统进化分析。结果表明: 6个居群刺参叶绿体基因组大小为156 108~156 193 bp, GC含量均为38.03%, 共注释到129~133个基因, 其中蛋白编码基因为87或88个, rRNA基因为6~8个, tRNA基因为36或37个。栽培刺参比野生刺参叶绿体基因组均多一个蛋白编码基因。以栽培刺参叶绿体基因组序列为参考, 与野生居群刺参进行序列比对, 共检测到36个SNP (single nucleotide polymorphism) 位点和10个InDel (insertion-deletion) 位点, SNP位点在基因间区和CDS区(coding sequences) 均有分布, 而InDel位点则全部分布于LSC区(large single-copy)。在13个样本叶绿体基因组的核苷酸多态性分析中检测到clpP1-exon3_clpP1-exon2、ycf1两个高多态区段, 可作为刺参DNA条形码候选区及分子标记开发。密码子偏好性分析揭示, 13个样本密码子偏好使用以A或T结尾的密码子。栽培与野生刺参叶绿体基因组在密码子数量方面存在差异。13个样本叶绿体基因组中检测到545个简单重复序列位点和498条散在重复序列。根据系统发育树各分支的支持率及聚类情况, 可将五加科8个属物种划分为四个分支, 刺参属以高支持率独立成支, 位于该树的中间位置, 分化时间比人参属晚, 与第四大分支互为姐妹群, 与鹅掌柴属亲缘关系最近。本研究增进了对刺参属及其近缘属进化的认识, 所获得遗传资源将为刺参属DNA条形码筛选、种质资源保护提供基因组学依据。

刺参  /  五加科  /  叶绿体基因组  /  对比分析  /  遗传变异  /  系统发育分析

Oplopanax elatus Nakai is a deciduous shrub within the Araliaceae family and is classified as a first-class protected plant in Jilin Province. To elucidate the structural characteristics of its chloroplast genome and phylogenetic relationships, this study conducted chloroplast genome sequencing of one cultivated individual and five wild populations of O. elatus, followed by comparative chloroplast genomic and phylogenetic analyses with published congeneric species of Oplopanax and allied genera of Araliaceae deposited in GenBank. The results revealed that the chloroplast genomes of the six O. elatus accessions ranged from 156 108-156 193 bp in length, with a uniform GC content of 38.03%. A total of 129-133 genes were annotated, comprising 87-88 protein-coding genes, 6-8 rRNA genes, and 36-37 tRNA genes. The chloroplast genome of cultivated O. elatus contained one additional protein-coding gene compared to those of wild accessions. Using the chloroplast genome sequence of cultivated O. elatus as reference, sequence alignment against wild populations identified 36 single nucleotide polymorphism (SNP) loci and 10 insertion-deletion (InDel) loci. SNPs were distributed in both intergenic spacers and coding sequences (CDS), whereas all InDels were restricted to the large single-copy (LSC) region. Nucleotide diversity (Pi) analysis of the 13 chloroplast genomes detected two hypervariable regions, clpP1-exon3_clpP1-exon2 and ycf1, which are proposed as candidate DNA barcodes and molecular markers for O. elatus. Analysis of codon preference indicated that all 13 samples exhibited a preference for codons terminating in A or T. Discrepancies in codon numbers were observed between cultivated and wild O. elatus chloroplast genomes. A total of 545 simple sequence repeat (SSR) loci and 498 dispersed repeat sequences were identified within the 13 chloroplast genomes. Phylogenetic reconstruction based on branch support values and clustering patterns partitioned the eight Araliaceae genera into four clades. The genus Oplopanax formed a highly supported monophyletic lineage positioned centrally within the tree, diverging subsequently to Panax and constituting a sister group to the fourth major clade, with its closest affinity to Schefflera. This investigation advances the understanding of evolutionary dynamics within Oplopanax and allied genera, with the acquired genomic resources providing a foundation for DNA barcode screening and germplasm conservation of the genus.

Oplopanax elatus  /  Araliaceae  /  chloroplast genome  /  comparative analysis  /  genetic variation  /  phylogenetic analysis
向光亿, 唐红鹃, 李慧芳, 李涵冰, 程林, 张永刚. 刺参叶绿体基因组特征与系统发育分析. 药学学报, 2026 , 61 (8) : 3186 -3198 . DOI: 10.16438/j.0513-4870.2026-0239
Guang-yi XIANG, Hong-juan TANG, Hui-fang LI, Han-bing LI, Lin CHENG, Yong-gang ZHANG. Characteristics and phylogenetic analysis of the chloroplast genome of Oplopanax elatus Nakai[J]. Acta Pharmaceutica Sinica, 2026 , 61 (8) : 3186 -3198 . DOI: 10.16438/j.0513-4870.2026-0239
正文
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刺参(Oplopanax elatus Nakai) 为五加科刺参属落叶灌木, 主要分布于中国吉林东部及辽宁东部的针阔混交林下, 在朝鲜半岛、俄罗斯远东地区亦有分布[1]。刺参属全球共有3个种, 中国仅分布刺参1种, 吉林省长白山地区及辽宁省东部山区是该物种核心种群聚集区[2]。其分布生境与日本刺参(Oplopanax japonicus Nakai) 和美洲刺参[Oplopanax horridus (Smith) Miq.] 存在显著分化。刺参作为我国珍贵药用植物, 因其根、茎、叶富含皂苷、多糖等多种生物活性成分[3], 现代药理学研究证实具有抗炎、抗氧化、免疫调节等功效[2, 4], 药用开发价值极高。但是受分布区域狭窄、生境退化与破碎化、人为过度采挖砍伐等多重因素叠加影响, 其野生资源锐减, 生存面临严重威胁。已被《中国生物多样性红色名录》《中国植物红皮书》《中国物种红色名录》等列为易危物种, 其资源保护与可持续利用已成为亟待解决的生态与产业问题。目前, 学界对刺参的研究主要集中在生物学特性研究、活性成分分离鉴定及药理作用验证等方面, 而针对刺参的遗传多样性保护机制和可持续利用策略的系统性研究仍较为薄弱。遗传多样性是生物多样性的重要组成部分, 反映物种内个体或群体的遗传变异水平, 是物种适应环境变化, 维持种群生存和繁衍能力的重要基础[5]。因此, 开展刺参种群遗传多样性评价, 为资源保育提供分子层面的科学依据, 具有重要的理论和实践意义。
叶绿体是植物细胞质内关键的半自主性细胞器, 叶绿体基因组是植物细胞器基因组的重要组成部分, 其编码基因组成与排列顺序相对稳定[6]。叶绿体基因组具有母系遗传特征, 兼具整体高度保守性和局部区域变异性, 且具备突变率适中、遗传信息量大及单倍体遗传等优势, 已被广泛应用于植物系统发育与进化、物种精准鉴定、资源引种驯化与分子育种等研究领域[7]。随着高通量测序技术的快速发展与成本降低, 叶绿体全基因组序列的获取效率大幅提升, 其在揭示植物属间、种间乃至居群间遗传变异规律的优势愈发凸显。此外, 通过叶绿体基因组结构对比分析, 可有效挖掘种间序列变异和识别高变异区以及重复序列等分子标记位点, 为物种遗传多样性评估与系统发育分析提供了精准技术手段[8]。这一技术路径已在药用植物中得到广泛应用, 通过叶绿体基因组分析为资源保护提供分子依据。刘巧珍等[9]对奇楠沉香叶绿体基因组进行比较分析, 筛选出trnD-trnY、trnT-trnL、trnF-ndhJ、petA-cemA、rpl32等5个高变区, 用作潜在的沉香属特异性DNA条形码; 尹光耀等[10]利用北苍术叶绿体基因组信息, 筛选出ccsA和trnC-GCA_petN为潜在的北苍术种内鉴别的特异DNA条形码, 并利用特异DNA条形码对不同产区北苍术样品开展种质资源鉴定及居群的遗传多样性分析; 陈锦豪等[11]利用黄精属叶绿体基因组筛选出的14个高变区序列作为候选分子标记, 对黄精属药用植物进行种间分子鉴定。
目前, 有关不同居群刺参叶绿体基因组序列特征、遗传变异规律及其在五加科中的系统发育地位尚未见相关报道, 严重限制了对该物种遗传背景的深入认识和资源保育工作的开展。为此, 本研究对栽培和野生刺参进行叶绿体全基因组测序与比对分析, 明确其叶绿体基因组的遗传差异, 阐明刺参群体间的遗传分化和遗传结构特点, 筛选出高变异区域以供分子标记开发和DNA条形码鉴定。同时, 整合五加科已公布叶绿体基因组数据, 从基因组结构、基因组成、序列变异等多个维度开展系统性比较分析, 明确刺参属在五加科中的系统发育位置以及与其他属种的亲缘关系。为刺参的遗传多样性保护、资源保育及种质资源创新提供坚实的分子基础与科学依据。
材料与方法
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植物材料及叶绿体基因组测序  2025年6~7月, 采集6个居群刺参幼嫩叶片(采集人: 向光亿、李慧芳)。其中, 栽培刺参居群源于吉林省白山市小东山林场, 引种至吉林省通化县大荒沟村种子播种5年(cs-01), 各样品采集具体信息如表1所示。采用密度梯度离心法分离叶绿体, 并用DNase I (Promega, Madison, USA) 消除叶绿体基因组DNA污染, 使用Nano-500超微量分光光度计(杭州奥盛仪器有限公司) 检测A260/A280比值范围为1.8~2.0, 随后经1.0%琼脂糖凝胶电泳检测, 显示条带清晰明亮且无拖尾即为合格。将合格DNA用于构建插入片段为350 bp的文库, 使用Illumina NovaSeq 6000测序技术进行PE150双端测序(上海凌恩生物科技有限公司)。使用Trimmomatic v0.39软件[12]对原始数据进行过滤, 过滤标准为: ①去除reads中的adapter序列; ②剪切前去除5′端含有非AGCT的碱基; ③修剪测序质量值小于Q20的reads末端; ④去除含N的比例达到10%的reads; ⑤舍弃去adapter及质量修剪后长度小于75 bp的小片段。
叶绿体基因组组装和注释  使用GetOrganelle v1.7.5软件[13]对过滤后的数据进行从头组装。以NCBI数据库上已公布的刺参叶绿体基因组序列(NC_085753) 作为参考, 确定叶绿体组装序列的起始位置和方向, 并确定叶绿体可能的分区结构, 得到最终的叶绿体基因组序列。利用在线注释工具GeSeq[14]对刺参叶绿体基因组基因进行注释, 选择默认参数预测各基因数量, 并将注释结果与四大数据库进行比较验证。对预测的初始基因去冗余, 对预测基因的起始密码子、终止密码子以及内含子/外显子边界进行人工校正。利用Organellar Genome DRAW软件[15]绘制刺参叶绿体基因组的环状物理图谱。
重复序列分析  使用MISA软件[16]对样本contig序列进行微卫星位点(simple sequence repeat, SSR) 分析。参数设置: 1-10 2-5 3-4 4-3 5-3 6-3; 两个SSR之间最小距离设置为100 bp。该参数设置基于以下原则: ①单核苷酸高阈值≥ 10, 可排除测序错误和poly-A尾干扰; ②二核苷酸≥ 5次可确保PCR扩增可行性和遗传多态性; ③三核苷酸≥ 4, 可确保编码区稳定性, 避免移码偏差; ④四-六核苷酸≥ 3, 可保证多态性。使用Primer3软件[17]对MISA识别获得的SSR序列设计引物。使用REPuter软件[18]对叶绿体基因组散在重复序列(scattered repetitive sequence) 进行分析, 鉴定类型为回文重复(palindromic repeats)、互补重复(complement repeats)、正向重复(forward repeats) 和反向重复(reverse repeats)。参数设置: 最短重复长度为30 bp, 最多碱基错配数为3, 最大重复次数为5 000。
SNP和InDel位点分析  以栽培刺参(cs-01) 叶绿体基因组序列作为参考, 利用MUMmer和LASTZ比对软件, 与5个野生居群刺参叶绿体基因组序列进行全局比对, 筛选野生刺参与栽培刺参序列之间潜在的SNP和InDel位点。比对标准: ①提取参考序列SNP位点两边各100 bp序列, 使用BLAT v35软件将提取的序列和组装结果进行比对, 验证SNP位点。去除比对长度小于101 bp的SNP位点, 最后得到可靠的SNP位点; ②取参考序列InDel位点上下游150 bp与样品的测序reads用BWA软件[19]及SAMtools进行比对验证, 经过滤得到可靠InDel位点。
密码子偏好性分析  使用cusp软件(EMBOSSv6.6.0.0)[20]检测6个新测序刺参及其同属、同科植物的密码子使用情况。通过计算同义密码子使用频率(relative synonymous codon usage, RSCU) 获得密码子的偏好性值。
基因组多态性分析、IR区收缩与扩张和结构比较分析  使用DnaSP v5.10软件[21]分析编码基因和非编码区的核苷酸多态性(nucleotide variability, Pi), 揭示基因组分歧热点区域。参数设置: 滑动窗口长度(window length) 设置为300 bp, 步长(step size) 为200 bp。使用在线分析软件IRscope[22]对13个五加科样本叶绿体基因组IR区边界基因进行比较分析。检测基因组中四个区域的边界收缩或扩张情况以及相关基因拷贝数的变化。以栽培刺参序列为参考, 使用在线软件mVISTA对叶绿体基因组序列多样性进行比较分析。
选择压力分析  通过同源蛋白编码基因的Ka/Ks比值分析评估正向选择压力。使用软件MUSCLE v3.8.31进行基因序列的比对, 用KaKs_Calculator 2.0计算KaKs。
系统发育分析  使用从GenBank数据库下载的27条已发表的五加科叶绿体基因组序列和本研究6条测序刺参叶绿体基因组序列进行系统发育分析。因伞形科与五加科同属于伞形目, 具有一定的亲缘关系又足够分化, 故本研究以伞形科药用植物防风(Saposhnikovia divaricata) 作为外类群(表2)。使用PhyML v3.0软件[23]以最大似然法(maximum likelihonnd, ML) 进行建树, 使用jModeltest v2.1.10对核苷酸替换模型进行评估, 通过AIC、BIC分值来寻找最佳模型, deltaic = 0的最优模型为GIR + I + G, bootstrap为1 000。
结果
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1　刺参叶绿体基因组特征分析
各居群刺参叶绿体基因组长度为156 108~156 193 bp, 其中FN居群刺参叶绿体基因组最小, BJG居群刺参叶绿体基因组最大, 栽培刺参(cs-01) 与XDS1、GMS居群的叶绿体基因组大小一致。各居群刺参叶绿体基因组均呈现典型的四分体结构(图1), 包括大单拷贝区(LSC区: 86 235~86 319 bp)、小单拷贝区(SSC区: 18 111~18 112 bp)、反向重复区(IR区: 25 880~25 881 bp)。其中LSC区变异幅度最大(相差84 bp), IR区和SSC区长度差异极小(相差1 bp)。此外, 6个居群的总GC含量表现出高度一致性(均为38.03%), LSC、SSC、IR区GC含量分别为36.24%~36.25%、32.09%~32.11%、43.08%, 符合大多数双子叶植物叶绿体基因组的GC分布特征。
各居群刺参叶绿体基因组总基因数为129~133个, 其中蛋白编码基因为87或88个, 核糖体RNA (rRNA) 基因为6~8个, 转运RNA (tRNA) 基因为36或37个。栽培刺参叶绿体基因组基因总数最多, 比野生居群刺参均多一个蛋白编码基因, 且在tRNA和rRNA基因数量上保持一致(BJF居群除外)。BJF居群刺参基因数量最少, 总基因数仅129个, 比其余居群刺参缺少1个tRNA和2个rRNA基因。整体来看, 栽培刺参在序列长度、GC含量上与XDS1野生居群刺参高度一致, 表明两者亲缘关系最近(表3)。
2　重复序列分析
13个五加科叶绿体基因组的SSR数量范围为37~46个, 共计545个SSR位点(图2)。其中, 单核苷酸329个、二核苷酸89个、三核苷酸28个、四核苷酸84个、五核苷酸14个、六核苷酸1个。SSR位点主要分布于LSC区域(86.42%), SSC区域(6.61%) 和IR区域(6.97%) 分布较少。本研究6个测序刺参叶绿体基因组的重复序列差异极小(2 bp), 仅存在于LSC区域。其中, 栽培刺参(cs-01) 与XDS1、FN野生居群刺参的SSR组成和分布完全一致。BJG、BJF、GMS居群刺参仅在单核苷酸重复序列数量和分布上存在微小差异(1 bp)。新测序刺参与同属参考样本相比, SSR数量最大仅差5个, 美洲刺参数量最多(46个)。与外属参考样本相比, 刺参SSR数量较多(41~46个), 人参的SSR总数最少(37个)。
此外, 还在13个五加科叶绿体基因组中检测到散在重复序列数量为34~58个, 共计498个(图3)。其中, 回文重复序列285个、正向重复序列196个、反向重复序列15个、互补重复序列2个(仅在狭叶罗伞中)。各散在重复序列长度各不相同, 长度为30~34 bp的数量最多(210个), 长度为45~49 bp的数量最少(6个)。本研究6个新测序刺参与同属日本刺参变种及前人测序刺参样本的散在重复序列类型和长度分布高度一致。与近缘属样本相比, 新测序刺参的散在重复序列总数显著低于其他亲缘物种, 短柄五加和狭叶罗伞的散在重复序列总数较多(分别为58个和51个)。
3　SNP和InDel位点分析
野生刺参与栽培刺参(cs-01) 叶绿体基因组多重比对后共鉴定到36个SNP和10个InDel差异位点(表4)。各样本SNP位点主要位于CDS区的ycf1和rps19基因, 以及psbA、matK、rps4、accD、ycf4、cemA、rp132间隔区附近。根据这些位点存在区域的序列长度可知, 插入缺失序列全部位于LSC区。从基因结构来看, 插入缺失序列有3个发生在基因间隔区, 位于atpF基因附近。其余InDel位点虽位于rps12和clpP1基因范围内, 但CDS区不存在InDel位点, 推测这些位点位于叶绿体基因组内含子区域, 且对蛋白质翻译框架无影响, 因此全部属于非编码区突变。其中, XDS1居群鉴定出2个InDel差异位点, 无SNP差异位点, 揭示该居群刺参与栽培刺参的亲缘关系最近。BJG居群差异最大(15个), 说明亲缘关系稍远。BJF、BJG、GMS野生居群的SNP构成高度一致, 揭示它们遗传分化小, 亲缘关系较近。
4　密码子偏好性分析
五加科13个样本叶绿体基因组的总密码子数量为25 979~26 579个(图4), 栽培刺参(cs-01) 密码子数量最多, 5个野生居群刺参密码子数量相同, 而前人测序刺参密码子总数最少。栽培刺参与野生刺参叶绿体基因组密码子数量差异可能反映了它们在遗传背景、环境适应性和人工选择压力等方面的不同。所有密码子中, 亮氨酸(Leu) 是最多的氨基酸, 半胱氨酸(Cys) 是最少的氨基酸。编码甲硫氨酸(Met) 和色氨酸(Trp) 的密码子ATG和TGG在这13个样本叶绿体基因组中均无密码子偏倚, RSCU值为1。13个样本叶绿体基因组中, 有29个密码子RSCU > 1, 其中有28个密码子的第三位碱基为A/T, 表明其叶绿体基因组偏好使用以A/T结尾的密码子。
5　叶绿体基因组结构比较分析
以栽培刺参(cs-01) 为参考, 利用mVISTA软件对13条叶绿体基因组进行全序列比对(图5)。结果表明, 刺参属植物整体序列高度保守, 编码区比非编码区保守, 反向重复区比单拷贝区保守。刺参属与其他属的主要区别位于非编码间隔区以及部分变异较快的基因, 主要识别出以下变异区段: trnH-psbA、matK、rps16-trnQ、trnS-trnG、accD、petN-psbM、ndhF、rpl32-trnL、ccsA、ycf1。其中LSC区域的trnH-psbA、trnS-trnG、accD以及SSC区的ndhF、rpl32-trnL、ycf1等高变异区域可用来开发刺参属物种鉴定或系统发育研究的分子标记。该叶绿体基因组结构对比分析图直观地揭示了从种内低变异到属间/科间高变异的进化梯度。
6　IR区的收缩与扩张
对13个叶绿体基因组进行了LSC-IRa、LSC-IRb、SSC-IRa和SSC-IRb四个边界的综合比较(图6)。在LSC-IRa区域, 美洲刺参因缺少trnH基因, 排列模式为rp12-psbA, 其余12个叶绿体基因组的边界排列模式为rpl2-trnH。在LSC-IRb区域, rps19和rpl2基因分别位于LSC-IRb的边界。在SSC-IRa区域, ycf1、trnN、rrn5基因位于这13个基因组的边界内, 其中ycf1基因延伸至IRa区域长度为1 473~1 649 bp, trnN和rrn5基因到SSC/IRa边界的距离为1 801~1 976和2 790 bp。在IRb-SSC区域, 栽培刺参(cs-01) 和狭叶罗伞、美洲刺参因缺少trnN基因, 其排列模式分别为ycf1-ndhF和rrn5-ndhF。其中ycf1基因分别扩展到SSC区域14 bp和7 bp, rrn5基因距离SSC区121 bp。其余样本叶绿体基因组排列模式均为trnN-ndhF。
7　叶绿体基因组多态性分析
为了进一步明确序列分化水平, 识别分化热点, 使用DnaSP v5.10软件分析了LSC、SSC、IRa、IRb及叶绿体基因组总量中的核苷酸多态性(Pi)。如图7可知, 这13个样本的Pi值为0~0.028, 平均值约为0.004。在这13个叶绿体基因组中共检测到trnT-GGU_psbD、trnT-UGU_trnL-UAA、clpP1-exon3_clpP1-exon2、rpl32_trnL-UAG、ycf1等6个分化区域, 多位于LSC区和SSC区, Pi值范围为0.016~0.028。其中trnT-GGU_psbD基因间区可能间接影响光合作用; trnT-UGU_trnL-UAA基因间区主要用作分子标记; clpP1-exon3_clpP1-exon2内含子区与抗逆性密切相关; rpl32_trnL-UAG是参与叶绿体蛋白质翻译系统的组件, 通常用作高变条形码; ycf1基因是被子植物叶绿体基因组中最长且变异最大的基因之一。其中clpP1-exon3_clpP1-exon2、ycf1 Pi值高于0.02为高度变异热点区, 是开发刺参特异性DNA条形码、用于物种鉴定和群体遗传学研究的最佳候选片段。
8　选择压力分析
由Ka/Ks热图可知(图8), 13个叶绿体基因组间无Ka/Ks > 1的红色区域, 表明近期未发生大规模正选择爆发。Ka/Ks峰值仅为0.817 (O. japonicus vs O. japonicus var. japonicus), 表明变种间出现稍多中性非同义差异。外属对照组与任何刺参属样本比较, Ka/Ks中位数为0.30~0.34, 呈净化选择, 这些分支在长期进化中已清除绝大多数有害非同义突变。在刺参属内, 刺参、日本刺参、美洲刺参间Ka/Ks比值为0.48~0.50, 表明属内分歧时间尚短, 尚未积累足够突变。7个刺参群体内部成对Ka/Ks为0.54~0.59, 完全不显著, 选择压力较弱, 说明居群间差异更多来自种群结构而非功能选择。
9　系统发育分析
基于叶绿体全基因组序列构建的ML系统发育树可知(图9), 该树各节点支持率为81%~100%, 说明结果可信度较高, 可将五加科8个属植物分为四个分支。天胡荽属植物聚为第一个分支, 位于该进化树的最基部, 与其余属亲缘关系最远, 揭示了天胡荽属较早从共同祖先中分离出来。楤木属和人参属植物共同构成第二分支, 形成一个独立的姐妹群。刺参属以高支持率独立成支, 位于该树的中间位置, 与第四大分支互为姐妹群, 与鹅掌柴属植物亲缘关系最近。其中美洲刺参最早分化, 并与日本刺参及其变种形成了明显的姐妹群关系。本土刺参整体聚在一起, 其中栽培刺参(cs-01) 与XDS1居群刺参亲缘关系最近, 揭示了从高海拔移栽到低海拔地区种植其遗传进化的稳定性。第四大分支是五加科核心进化支, 位于进化树底部, 包括鹅掌柴属、树参属、罗伞属、五加属等13个植物。其中鹅掌柴属最早分化, 树参属与罗伞属植物三叶罗伞聚在一起, 并与其余罗伞属植物构成姐妹关系。五加属位于进化树的最末端, 与罗伞属亲缘关系最近。
讨论
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本研究对栽培和野生刺参个体进行叶绿体因组测序和全面分析, 结果显示6个刺参的叶绿体基因组高度保守, 且均为环状四分体结构, 符合被子植物叶绿体基因组结构特征[24]。各叶绿体基因组的大小差异主要在LSC区, 这与五加科植物叶绿体基因组结构分析中的研究结果一致[25]。说明五加科植物叶绿体基因组LSC区变异普遍较高。
叶绿体基因组中的简单重复序列不仅含量丰富, 还具有单亲遗传特点, 已被广泛应用于遗传图谱构建、靶基因校准和定位研究中的分子标记[26, 27]。本研究发现刺参叶绿体基因组SSR位点主要分布于LSC区, 这一特征与苦参属[28]、甘草属[29]、白尾草属[30]等多种药用植物研究结果相似, 暗示其可能参与刺参的环境适应性进化。其中, 单核苷酸重复类型最为常见, 这一特征与狭叶罗伞[31]、黄芪[32]、保亭树参[33]、梧桐属[34]等药用植物重复序列分析结果相似。密码子偏好性分析显示这13个五加科植物均偏好使用以A/T结尾的密码子, 这与狼尾草属[35]、榕属[36]、肉苁蓉属[37]等植物叶绿体基因组密码子偏好性结果一致, 说明不同物种间叶绿体基因组密码子使用偏好性存在一定相似性。
IR区的收缩与扩张被认为是叶绿体基因组中重要的进化事件, 其收缩与扩张是引起植物叶绿体基因组大小改变的原因之一[38]。本研究IR区边界分析显示, 刺参属相比于外属对照组, 表现出独特的进化特征。在IR-SSC边界(如ycf1、ndhF基因的扩张与收缩) 存在显著变异, 反映了不同属间的进化动态, 相似的结果也见于在天南星科[39]、芭蕉科[40]、千屈菜科[41]植物叶绿体基因组边界分析研究中。此外, 选择压力分析显示, 刺参属与外属比较Ka/Ks值远小于1, 呈现出强烈的净化选择。这表明五加科植物在长期的进化历程中, 其叶绿体基因组中绝大多数有害的非同义突变已被清除, 维持了光合作用等核心蛋白功能的高度保守性。
基于叶绿体基因组全序列比对分析可知, 刺参属植物整体序列高度一致, 在LSC (trnH-psbA、trnS-trnG、accD)、SSC区域(ndhF、rpl32-trnL、ycf1) 存在变异。其中, 编码区比非编码区更保守, 反向重复区比单拷贝区更加保守, 这一结果与Fang等[30]在白鼠尾草叶绿体基因组分析中的结果一致。此外, 在叶绿体基因组核苷酸多态性分析中, 筛选出clpP1-exon3_clpP1-exon2和ycf1高度变异区, 分别位于LSC和SSC区域。综上所述, 两个分析均表明刺参属IR区较为保守, 变异多发生在LSC和SSC区域, 这与Zhang等[42]在柴胡属药用植物叶绿体基因组研究中的结果相似, 同时也与其他被子植物叶绿体基因组序列变异模式相同[43, 44]。近年来, ycf1被认为是陆生植物中最具潜力的条形码候选区段[45]。筛选出的高变区段, 可作为刺参属DNA条形码候选区及开发多态性分子标记。
明确栽培品种的种质来源是中药材规范化种植的前提。在本土刺参居群中, SNP和InDel多态性分析精准揭示了栽培刺参(cs-01) 的系统发生位置。结果显示, 栽培刺参与XDS1野生居群刺参叶绿体基因组大小一致, 且二者比对仅存在2个InDel位点, 表明两者亲缘关系最近, 证明野生刺参从高海拔原生境引种至低海拔地区进行人工种植后, 其叶绿体基因组序列未发生剧烈变异, 展现出了极高的遗传进化稳定性和良好的环境适应能力。揭示了在低海拔区域对野生刺参迁地种植的可行性, 对其资源保育和可持续利用具有重要意义。
基于34条叶绿体全基因组构建的ML树将五加科划分为四个分支, 这与五加科植物叶绿体基因组系统发育的结果相似[46]。刺参属内存在明显的种内及种间多样性, 美洲刺参位于刺参属的基部, 随后分化出日本刺参和本土刺参。这一拓扑结构生动地反映了“东亚-北美间断分布”植物地理学模式, 结合Li等[47]关于五加科植物在北半球的演化、辐射分化与第三纪气候骤变及地质构造事件密切相关的研究观点, 推测刺参属的共同祖先曾属于第三纪孑遗植物区系, 在气候温暖时, 通过白令陆桥在亚洲与北美洲之间发生了广泛的洲际迁移。随第四纪冰期的到来及全球气候骤冷, 冰川阻断了连接通道, 形成了严格的地理隔离, 阻断了东亚与北美居群间的基因交流, 两个种群沿着不同的演化轨迹发生异域物种形成, 导致了美洲刺参的早期分化。而在东亚分支内部, 本土刺参与日本刺参的高度亲缘关系及其地域变种的分化, 暗示了东北亚地区在冰期后可能存在物种的辐射扩散或一定的基因交流通道。此分类结构不仅为刺参属的系统进化提供了新的见解, 同时也为进一步的生物地理研究提供了基础。
此外, 本研究结合野外调查和上述分析结果, 提出刺参野生居群的针对性保护建议: ①基于SNP和InDel位点分析结果, 验证XDS1居群刺参与栽培刺参亲缘关系最近, 且遗传多样性丰富, 应设置保护区域, 优先保护; ②在刺参核心分布区域设置清晰警示标识, 明确标注禁止采挖、禁止放牧等管控要求; ③加强刺参科普宣传, 并进行刺参野生资源保育和引种驯化等工作, 可选择XDS1居群作为种质资源来源, 模拟原生境进行移栽, 构建保护与利用良性循环。
综上所述, 本研究为濒危珍稀药用植物刺参的物种鉴定、资源保育及种质资源创新提供了坚实的分子数据支撑。但仅从叶绿体基因组水平上进行分析, 且未覆盖刺参全部分布区, 未来研究可扩大采样量, 并进一步结合转录组、代谢组、核基因组等多组学技术, 深入探究栽培与野生刺参在药效物质生物合成途径上的差异机制, 以期为刺参优良品种的选育、药用活性成分的定向培育及中药资源的可持续开发利用提供全面的科学依据。

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2026年第61卷第8期
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doi: 10.16438/j.0513-4870.2026-0239
  • 接收时间：2026-03-05
  • 首发时间：2026-09-21
  • 出版时间：2026-08-12
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  • 收稿日期：2026-03-05
  • 修回日期：2026-05-12
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    吉林农业大学中药材学院, 吉林 长春 130118

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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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