Article(id=1317485690921796600, tenantId=1146029695717560320, journalId=1316781310003478668, issueId=1317485675247685791, articleNumber=null, orderNo=null, doi=10.11983/CBB25008, pmid=null, cstr=32102.14.CBB25008, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1736956800000, receivedDateStr=2025-01-16, revisedDate=null, revisedDateStr=null, acceptedDate=1746547200000, acceptedDateStr=2025-05-07, onlineDate=1792042666415, onlineDateStr=2026-10-15, pubDate=1767974400000, pubDateStr=2026-01-10, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1792042666415, onlineIssueDateStr=2026-10-15, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1792042666415, creator=13701087609, updateTime=1792042666415, updator=13701087609, issue=Issue{id=1317485675247685791, tenantId=1146029695717560320, journalId=1316781310003478668, year='2026', volume='61', issue='1', pageStart='1', pageEnd='169', issueExtLink='null', onlineDate='null', pubDate='1767974400000', pubDateStr='2026-01-10', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=1, specialIssue=null, createTime=1792042662679, creator='13701087609', updateTime=1792140573918, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1317896344832946412, tenantId=1146029695717560320, journalId=1316781310003478668, issueId=1317485675247685791, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1317896344832946413, tenantId=1146029695717560320, journalId=1316781310003478668, issueId=1317485675247685791, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=26, endPage=36, ext={EN=ArticleExt(id=1317485691211203578, articleId=1317485690921796600, tenantId=1146029695717560320, journalId=1316781310003478668, language=EN, title=Expression Pattern and Metabolic Correlation Analysis of TCP Gene Family in Bergenia purpurascens, columnId=1317485691135706105, journalTitle=Chinese Bulletin of Botany, columnName=RESEARCH ARTICLES, runingTitle=null, highlight=null, articleAbstract=
INTRODUCTION:

The TCP protein family is a plant-specific group of transcription factors known to regulate key biological processes, including growth and development, as well as stress responses. Despite their critical roles, the TCP gene family in Bergenia purpurascens remains uncharacterized. This study aims to systematically identify and analyze the BpTCP gene family in B. purpurascens using transcriptome-based bioinformatics approaches, providing new insights into their potential functions in cold adaptation and secondary metabolism.

RATIONALE:

B. purpurascens exhibits remarkable resilience to abiotic stresses, particularly cold, and contains abundant secondary metabolites. Given the documented roles of TCP genes in stress responses and metabolic regulation in other plants, we hypothesized that BpTCP genes may contribute to these traits. A comprehensive analysis of this gene family could reveal novel mechanisms underlying stress adaptation and metabolite synthesis, supporting future genetic improvement and biotechnological applications.

RESULTS:

Through transcriptome-based bioinformatics analysis, we identified 16 BpTCP genes in B. purpurascens, which were phylogenetically classified into two major groups, with all members containing conserved TCP domains and closely related proteins sharing similar motif patterns. Tissue-specific expression profiling revealed distinct spatial expression patterns across different tissues, suggesting functional diversification among family members. Notably, partial genes, including BpTCP10, BpTCP1 and BpTCP12, exhibited significant expression changes under cold stress, implying their potential cold-responsive roles. Furthermore, expression levels of specific BpTCP genes correlated significantly with accumulation of various secondary metabolites, particularly flavonoids and phenolics, suggesting their regulatory involvement in metabolic pathways.

CONCLUSION:

This study provides the first genome-wide characterization of the BpTCP gene family in B. purpurascens, demonstrating its potential roles in growth and development as well as cold stress response, and secondary metabolism. The differential expression of BpTCP genes under stress and their correlation with metabolite levels lay a foundation for future functional studies.

, authors=Jingyu Chen1, Wenqing Wang1, Shiyu Luo2, Luxiang Yang1, Huijun Wang1, Tianyu Wu1, Qiankun Zhu1, *, authorsList=Jingyu Chen, Wenqing Wang, Shiyu Luo, Luxiang Yang, Huijun Wang, Tianyu Wu, Qiankun Zhu, authorCompany=null, correspAuthors=Qiankun Zhu, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, 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=1317485695321620487, articleId=1317485690921796600, tenantId=1146029695717560320, journalId=1316781310003478668, language=CN, title=岩白菜TCP基因家族的表达模式及代谢关联分析, columnId=1317485691316061179, journalTitle=植物学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

TCP蛋白家族是植物特有的一类转录因子家族,在植物生长发育及胁迫响应过程中发挥重要作用。为阐明岩白菜(Bergenia purpurascens)BpTCP基因家族的功能,基于转录组测序数据,利用生物信息学方法对岩白菜BpTCP基因家族进行系统鉴定与分析。共鉴定出16个BpTCP基因,可分为2大类,所有BpTCP基因均含有保守的TCP结构域,相同进化枝的BpTCP蛋白所含基序类型相似。表达模式分析表明,不同BpTCP基因在不同组织中的表达水平存在差异。低温胁迫条件下,BpTCP10、BpTCP1和BpTCP12的表达出现显著变化。BpTCP基因家族表达水平与次级代谢物含量的相关性分析显示,部分BpTCP基因的表达与黄酮类和酚类等多种代谢物含量间显著相关。研究结果为深入探究BpTCP基因在岩白菜生长发育、低温胁迫响应及次生代谢合成途径中的生物学功能奠定了基础。

, authors=陈靖彧1, 王文庆1, 罗诗语2, 杨路祥1, 汪慧骏1, 吴天宇1, 朱乾坤1, *, authorsList=陈靖彧, 王文庆, 罗诗语, 杨路祥, 汪慧骏, 吴天宇, 朱乾坤, authorCompany=null, correspAuthors=朱乾坤, authorNote=

作者贡献声明

陈靖彧:完成实验、分析数据及撰写论文;王文庆、罗诗语、杨路祥和汪慧骏:分析数据;吴天宇:论文修改润色;朱乾坤:审阅及修改论文。

朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

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朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

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朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

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Nat Prod Res32, 668–675, articleTitle=null, refAbstract=null), Reference(id=1317485703517290599, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=null, rfOrder=32, authorNames=null, journalName=null, refType=null, unstructuredReference=Zhang XB, Yu F, Lyu X, Chen JY, Zeng HY, Xu NM, Wu YF, Zhu QK (2023). Transcriptome profiling of Bergenia purpurascens under cold stress. 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Afr J Biotechnol10, 8166–8169, articleTitle=null, refAbstract=null), Reference(id=1317485703668285545, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, doi=null, pmid=null, pmcid=null, year=null, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=null, rfOrder=34, authorNames=null, journalName=null, refType=null, unstructuredReference=Zhu QK, Wu YF, Zhang XB, Xu NM, Chen JY, Lyu X, Zeng HY, Yu F (2024). Metabolomic and transcriptomic analyses reveals candidate genes and pathways involved in secondary metabolism in Bergenia purpurascens. BMC Genomics25, 1083, articleTitle=null, refAbstract=null)], funds=null, companyList=[AuthorCompany(id=1317485695573278728, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, xref=1, ext=[AuthorCompanyExt(id=1317485695581667337, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695573278728, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1College of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China), AuthorCompanyExt(id=1317485695594250250, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695573278728, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1西南交通大学生命科学与工程学院,成都 610031)]), AuthorCompany(id=1317485695665553419, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, xref=2, ext=[AuthorCompanyExt(id=1317485695673942028, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695665553419, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2Chengdu Shishi High School of Sichuan Province, Chengdu 610041, China), AuthorCompanyExt(id=1317485695682330637, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695665553419, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2四川省成都市石室中学,成都 610041)])], figs=[ArticleFig(id=1317485697972420665, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Figure 1, caption=The phylogenetic tree of Arabidopsis thaliana, Oryza sativa, and Bergenia purpurascens TCP gene family, figureFileSmall=nTy+fJPrziqf12urvIw1vA==, figureFileBig=0Br5v5a/VdbbmSSmnO5Wlg==, tableContent=null), ArticleFig(id=1317485698052112442, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=图1, caption=拟南芥、水稻和岩白菜TCP基因家族的系统进化树

进化树的分支颜色及填充底色表示不同的TCP亚家族。At:拟南芥;Os:水稻;Bp:岩白菜

, figureFileSmall=nTy+fJPrziqf12urvIw1vA==, figureFileBig=0Br5v5a/VdbbmSSmnO5Wlg==, tableContent=null), ArticleFig(id=1317485698240856123, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Figure 2, caption=Analysis of conserved motifs and protein interaction network of Bergenia purpurascens TCP gene family, figureFileSmall=wWYnMOO8I+b9YjWeOcvkxQ==, figureFileBig=NxMJ8Nlj64d7VdiOBNhQ0w==, tableContent=null), ArticleFig(id=1317485698324742204, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=图2, caption=岩白菜TCP基因家族的保守基序和蛋白互作网络分析

(A)岩白菜TCP基因家族的保守基序分析(左列:BpTCP基因家族成员;中列:保守基序(motif 1–10)在基因上的分布;右列:motif 1–10的序列信息);(B)蛋白互作网络分析(每个节点表示1个蛋白,2个蛋白之间连线越多表明相互作用越强)

, figureFileSmall=wWYnMOO8I+b9YjWeOcvkxQ==, figureFileBig=NxMJ8Nlj64d7VdiOBNhQ0w==, tableContent=null), ArticleFig(id=1317485698404433981, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Figure 3, caption=Expression patterns of Bergenia purpurascens TCP gene family in different tissues and under cold stress, figureFileSmall=9+AYAIKSGqbaCFafdcPnKw==, figureFileBig=kdxCbyJWt+u26wqEkEnXtQ==, tableContent=null), ArticleFig(id=1317485698475737150, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=图3, caption=岩白菜TCP基因家族在不同组织和低温胁迫下的表达模式

(A)岩白菜TCP基因家族在根、茎和叶中的表达模式;(B)岩白菜TCP基因家族在低温胁迫(4°C,6小时)下的表达模式。CK:对照

, figureFileSmall=9+AYAIKSGqbaCFafdcPnKw==, figureFileBig=kdxCbyJWt+u26wqEkEnXtQ==, tableContent=null), ArticleFig(id=1317485698547040319, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Figure 4, caption=qRT-PCR validation of 6 BpTCP genes, figureFileSmall=evxrtvcBB3BgJ9+pwSgCMw==, figureFileBig=4aRCdsZJGa4wrNDJgATQbg==, tableContent=null), ArticleFig(id=1317485698614149184, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=图4, caption=6个BpTCP基因的qRT-PCR验证

以正常条件为对照(CK),低温胁迫处理为4°C下处理6小时。统计分析方法为ANOVA。*表示显著正相关(P<0.05),**表示非常显著正相关(P<0.01),***表示极显著正相关(P<0.001)。

, figureFileSmall=evxrtvcBB3BgJ9+pwSgCMw==, figureFileBig=4aRCdsZJGa4wrNDJgATQbg==, tableContent=null), ArticleFig(id=1317485698677063745, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Figure 5, caption=Heat map of the correlation between Bergenia purpurascens TCP gene family expression level and secondary metabolites content, figureFileSmall=mB+3MuEhRZDjyLaXGOcDKw==, figureFileBig=GuMF6F3lMrC7xeYycCZEqg==, tableContent=null), ArticleFig(id=1317485698765144130, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=图5, caption=岩白菜TCP基因表达水平与次级代谢物含量的相关性热图

采用Pearson相关性分析方法。*表示显著正相关(P<0.05),**表示非常显著正相关(P<0.01),***表示极显著正相关(P<0.001)。

, figureFileSmall=mB+3MuEhRZDjyLaXGOcDKw==, figureFileBig=GuMF6F3lMrC7xeYycCZEqg==, tableContent=null), ArticleFig(id=1317485698832252995, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=EN, label=Table 1, caption=

Predicted analysis of the physicochemical properties of Bergenia purpurascens TCP gene family

, figureFileSmall=null, figureFileBig=null, tableContent=
Gene IDGene nameAmino acids length(aa)Molecular weight(Da)Isoelectric pointAverage hydrophilicitySubcellular localization
TRINITY_DN14831_c0_g2BpTCP146350131.137.11–0.635Nucleus
TRINITY_DN2391_c0_g1BpTCP239542190.808.39–0.613Nucleus
TRINITY_DN2391_c0_g3BpTCP339242335.396.27–0.718Nucleus
TRINITY_DN14831_c0_g1BpTCP447250863.396.75–0.749Nucleus
TRINITY_DN2391_c0_g4BpTCP541744550.117.00–0.632Nucleus
TRINITY_DN46292_c0_g1BpTCP637239650.796.98–0.403Nucleus
TRINITY_DN4014_c0_g1BpTCP740142386.515.45–0.459Nucleus
TRINITY_DN2391_c0_g2BpTCP840743504.956.59–0.587Nucleus
TRINITY_DN12413_c0_g1BpTCP935940139.246.36–0.822Nucleus
TRINITY_DN1411_c0_g2BpTCP1035138394.766.02–0.766Nucleus
TRINITY_DN16929_c0_g1BpTCP1117719247.839.52–0.555Nucleus
TRINITY_DN1769_c0_g1BpTCP1227028218.739.71–0.334Nucleus
TRINITY_DN5850_c0_g2BpTCP1355358720.356.51–0.729Nucleus
TRINITY_DN5850_c0_g1BpTCP1454457482.266.61–0.678Nucleus
TRINITY_DN84293_c0_g1BpTCP1520521920.727.83–0.460Nucleus
TRINITY_DN5961_c0_g1BpTCP1630332595.865.57–0.364Nucleus
), ArticleFig(id=1317485698916139076, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, language=CN, label=表1, caption=

岩白菜TCP基因家族的理化性质预测分析

, figureFileSmall=null, figureFileBig=null, tableContent=
Gene IDGene nameAmino acids length(aa)Molecular weight(Da)Isoelectric pointAverage hydrophilicitySubcellular localization
TRINITY_DN14831_c0_g2BpTCP146350131.137.11–0.635Nucleus
TRINITY_DN2391_c0_g1BpTCP239542190.808.39–0.613Nucleus
TRINITY_DN2391_c0_g3BpTCP339242335.396.27–0.718Nucleus
TRINITY_DN14831_c0_g1BpTCP447250863.396.75–0.749Nucleus
TRINITY_DN2391_c0_g4BpTCP541744550.117.00–0.632Nucleus
TRINITY_DN46292_c0_g1BpTCP637239650.796.98–0.403Nucleus
TRINITY_DN4014_c0_g1BpTCP740142386.515.45–0.459Nucleus
TRINITY_DN2391_c0_g2BpTCP840743504.956.59–0.587Nucleus
TRINITY_DN12413_c0_g1BpTCP935940139.246.36–0.822Nucleus
TRINITY_DN1411_c0_g2BpTCP1035138394.766.02–0.766Nucleus
TRINITY_DN16929_c0_g1BpTCP1117719247.839.52–0.555Nucleus
TRINITY_DN1769_c0_g1BpTCP1227028218.739.71–0.334Nucleus
TRINITY_DN5850_c0_g2BpTCP1355358720.356.51–0.729Nucleus
TRINITY_DN5850_c0_g1BpTCP1454457482.266.61–0.678Nucleus
TRINITY_DN84293_c0_g1BpTCP1520521920.727.83–0.460Nucleus
TRINITY_DN5961_c0_g1BpTCP1630332595.865.57–0.364Nucleus
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岩白菜TCP基因家族的表达模式及代谢关联分析
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陈靖彧 1 , 王文庆 1 , 罗诗语 2 , 杨路祥 1 , 汪慧骏 1 , 吴天宇 1 , 朱乾坤 1, *
植物学报 | 研究论文 2026,61(1): 26-36
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植物学报 |研究论文 2026 , 61 (1) : 26 -36
岩白菜TCP基因家族的表达模式及代谢关联分析
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朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

"}, bioImg=null, bioContent=

朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1317485695573278728, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, xref=1, ext=[AuthorCompanyExt(id=1317485695581667337, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695573278728, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1College of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China), AuthorCompanyExt(id=1317485695594250250, tenantId=1146029695717560320, journalId=1316781310003478668, articleId=1317485690921796600, companyId=1317485695573278728, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1西南交通大学生命科学与工程学院,成都 610031)])])]
陈靖彧1, 王文庆1, 罗诗语2, 杨路祥1, 汪慧骏1, 吴天宇1, 朱乾坤1, *
作者信息
  • 1西南交通大学生命科学与工程学院,成都 610031
  • 2四川省成都市石室中学,成都 610041
通讯作者:
作者简介:

作者贡献声明

陈靖彧:完成实验、分析数据及撰写论文;王文庆、罗诗语、杨路祥和汪慧骏:分析数据;吴天宇:论文修改润色;朱乾坤:审阅及修改论文。

朱乾坤,博士,副教授,硕士生导师;入选四川省高层次人才计划,四川省细胞生物学会理事/遗传学会理事/生物化学与分子生物学会青年委员;主要从事植物分子细胞与生物合成相关研究,承担多项国家/省部级科研项目,研究论文发表在Nature Plants、Chinese Journal of Chemistry、BMC Genomics、Plant Molecular Biology和Plant Physiology and Biochemistry等国内外学术期刊。

Expression Pattern and Metabolic Correlation Analysis of TCP Gene Family in Bergenia purpurascens
Jingyu Chen1, Wenqing Wang1, Shiyu Luo2, Luxiang Yang1, Huijun Wang1, Tianyu Wu1, Qiankun Zhu1, *
Affiliations
  • 1College of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
  • 2Chengdu Shishi High School of Sichuan Province, Chengdu 610041, China
出版时间: 2026-01-10 doi: 10.11983/CBB25008
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TCP蛋白家族是植物特有的一类转录因子家族,在植物生长发育及胁迫响应过程中发挥重要作用。为阐明岩白菜(Bergenia purpurascens)BpTCP基因家族的功能,基于转录组测序数据,利用生物信息学方法对岩白菜BpTCP基因家族进行系统鉴定与分析。共鉴定出16个BpTCP基因,可分为2大类,所有BpTCP基因均含有保守的TCP结构域,相同进化枝的BpTCP蛋白所含基序类型相似。表达模式分析表明,不同BpTCP基因在不同组织中的表达水平存在差异。低温胁迫条件下,BpTCP10、BpTCP1和BpTCP12的表达出现显著变化。BpTCP基因家族表达水平与次级代谢物含量的相关性分析显示,部分BpTCP基因的表达与黄酮类和酚类等多种代谢物含量间显著相关。研究结果为深入探究BpTCP基因在岩白菜生长发育、低温胁迫响应及次生代谢合成途径中的生物学功能奠定了基础。

岩白菜  /  TCP基因家族  /  基因家族鉴定  /  生物信息学
INTRODUCTION:

The TCP protein family is a plant-specific group of transcription factors known to regulate key biological processes, including growth and development, as well as stress responses. Despite their critical roles, the TCP gene family in Bergenia purpurascens remains uncharacterized. This study aims to systematically identify and analyze the BpTCP gene family in B. purpurascens using transcriptome-based bioinformatics approaches, providing new insights into their potential functions in cold adaptation and secondary metabolism.

RATIONALE:

B. purpurascens exhibits remarkable resilience to abiotic stresses, particularly cold, and contains abundant secondary metabolites. Given the documented roles of TCP genes in stress responses and metabolic regulation in other plants, we hypothesized that BpTCP genes may contribute to these traits. A comprehensive analysis of this gene family could reveal novel mechanisms underlying stress adaptation and metabolite synthesis, supporting future genetic improvement and biotechnological applications.

RESULTS:

Through transcriptome-based bioinformatics analysis, we identified 16 BpTCP genes in B. purpurascens, which were phylogenetically classified into two major groups, with all members containing conserved TCP domains and closely related proteins sharing similar motif patterns. Tissue-specific expression profiling revealed distinct spatial expression patterns across different tissues, suggesting functional diversification among family members. Notably, partial genes, including BpTCP10, BpTCP1 and BpTCP12, exhibited significant expression changes under cold stress, implying their potential cold-responsive roles. Furthermore, expression levels of specific BpTCP genes correlated significantly with accumulation of various secondary metabolites, particularly flavonoids and phenolics, suggesting their regulatory involvement in metabolic pathways.

CONCLUSION:

This study provides the first genome-wide characterization of the BpTCP gene family in B. purpurascens, demonstrating its potential roles in growth and development as well as cold stress response, and secondary metabolism. The differential expression of BpTCP genes under stress and their correlation with metabolite levels lay a foundation for future functional studies.

Bergenia purpurascens  /  TCP gene family  /  gene family identification  /  bioinformatics
陈靖彧, 王文庆, 罗诗语, 杨路祥, 汪慧骏, 吴天宇, 朱乾坤. 岩白菜TCP基因家族的表达模式及代谢关联分析. 植物学报, 2026 , 61 (1) : 26 -36 . DOI: 10.11983/CBB25008
Jingyu Chen, Wenqing Wang, Shiyu Luo, Luxiang Yang, Huijun Wang, Tianyu Wu, Qiankun Zhu. Expression Pattern and Metabolic Correlation Analysis of TCP Gene Family in Bergenia purpurascens[J]. Chinese Bulletin of Botany, 2026 , 61 (1) : 26 -36 . DOI: 10.11983/CBB25008
岩白菜(Bergenia purpurascens)隶属虎耳草科(Saxifragaceae)岩白菜属(Bergenia),是一种常绿多年生草本植物,主要分布于中亚和东亚,偏好生长在岩石缝隙或阴湿环境中,具有很强的环境适应性(吕秀立等,2018)。岩白菜由于耐寒、耐阴且叶色变化丰富,被大量应用于园林绿化与景观设计,尤其适合在林下、花坛边缘和岩石园中作为地被植物栽种(Zhang et al.,2018)。此外,岩白菜在传统中药中也有广泛应用,其根状茎和全草均可入药,主要用于治疗呼吸和泌尿系统相关疾病(李文春等,2006)。研究发现,岩白菜富含多种生物活性成分,如岩白菜素、槲皮素及儿茶素,这些化合物赋予岩白菜抗氧化、抗炎及抗菌等多种功效(Zhang et al.,2011)。
TCP蛋白家族是植物特有的一类转录因子家族,命名基于4个已被鉴定的蛋白质:来自玉米(Zea mays)的TB1(teosinte branched1)、来自金鱼草(Antirrhinum majus)的CYC(cycloidea)以及来自水稻(Oryza sativa)的增殖细胞因子1和2(PCF1和PCF2)(Cubas et al.,1999;Martin-Trillo and Cubas,2010)。该家族成员包含由约59 aa组成的保守TCP结构域,该区域含有螺旋-环-螺旋(basic helix-loop-helix,bHLH)结构,参与DNA结合和二聚化(Kosugi and Ohashi,1997)。根据蛋白结构域序列特征和系统发育关系,TCP基因家族成员可分为两大分支:Class I和Class II,Class I亦称PCF类或TCP-P类,Class II又进一步分为CYC/TB1和CIN亚类,两类蛋白之间最显著的差异是I类蛋白质相对于II类蛋白质在TCP结构域中缺失了4个氨基酸(Martin-Trillo and Cubas,2010)。
近年研究表明,TCP基因家族在植物生长发育过程中发挥重要作用。在拟南芥(Arabidopsis thaliana)中,AtTCP16参与花粉的早期发育(Takeda et al.,2006);AtTCP14在种子萌发过程中调节胚胎的生长潜力(Tatematsu et al.,2008);AtTCP20是参与细胞分裂、伸长和分化的许多效应器的共同调节剂(Hervé et al.,2009);AtTCP20和AtTCP22作为早晨基因CCA1的激活剂,对于调节拟南芥生物钟有积极作用(Wu et al.,2016)。豌豆(Pisum sativum)中的PsBRC1属于CYC/TB1类TCP成员,其突变后豌豆侧枝的数量增多(Braun et al.,2012)。此外,TCP基因还参与植物激素信号转导以及多种生物和非生物胁迫的响应。例如,陆地棉(Gossypium hirsutum)的GhTCP14能调控生长素响应和载体蛋白基因的表达(Wang et al.,2013)。AtTCP3可以激活生长素信号阻遏基因IAA3/SHY2的表达(Koyama et al.,2010)。在苹果(Malus domestica)中,过表达MdTCP46可抑制MdABI5的转录活性,降低苹果对脱落酸的敏感性和对干旱胁迫的抗性(Liu et al.,2022)。
迄今,对岩白菜的研究主要集中在其药理价值和化学成分,分子生物学和基因组学方面的报道较少,且关于岩白菜TCP基因家族的相关研究尚未见报道。基于之前获得的岩白菜转录组数据(Zhang et al.,2023),本研究通过生物信息学方法对鉴定出的BpTCP基因家族成员的蛋白理化性质、序列特征、进化关系和表达模式等进行分析,探究BpTCP基因家族在岩白菜生长发育和低温胁迫响应中可能的生物学功能,并分析了BpTCP基因家族表达水平与次级代谢物含量的相关性,为进一步探讨BpTCP基因家族在次生代谢调控中的作用奠定理论基础。
本研究使用的植物样本采自四川省汶川县,通过ITS2和psbA-trnH序列的形态学鉴定和DNA分子鉴定,确认该样本为三年生岩白菜(Bergenia purpurascens(Hook.f. et Thoms.)Engl.)(Zhang et al.,2023)。将采集的岩白菜种植于泥炭土:蛭石=3:1(v/v)的混合土中,在22°C长日照条件下(光周期16小时光照/8小时黑暗,光照强度70 µmol·m–2·s–1)培养。岩白菜3种组织(根、茎、叶)及经低温处理的叶(处理温度:4°C,处理时间:6小时)的转录组数据由本课题组前期测序获得(Zhang et al.,2023)。
从Pfam蛋白家族数据库(http://pfam.sanger.ac.uk/)下载TCP结构域(PF03634)的隐马尔可夫模型(HMM)文件,利用软件HMMER 3.0从岩白菜转录组数据的蛋白质序列中搜索潜在的TCP基因。随后利用在线工具NCBI CDD(https://www.ncbi.nlm.nih.gov/cdd/)验证BpTCP蛋白结构域的完整性。利用ExPASy网站(https://www.ExPASy.org/)预测BpTCP蛋白的理化性质,包括分子量、等电点和亲水性,参数设置为默认值。使用Plant-mPLoc网站(http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/)预测BpTCP蛋白的亚细胞定位。
从TAIR网站(https://www.arabidopsis.org/)下载拟南芥24个TCP基因及从水稻信息资源网站(https://rice.uga.edu/)下载水稻22个TCP基因作为参考,使用DNAMAN 9.0软件对岩白菜、拟南芥和水稻的TCP基因进行多序列比对,并使用软件MEGA7.0采用邻接法(neighbor-joining method,NJ)进行1 000个引导重复来构建系统发育树。使用MEME在线工具(http://alternate.meme-suite.org/tools/meme)预测BpTCP蛋白的保守基序,最大基序设置为10。利用在线网站tvbot(https://www.chiplot.online/tvbot.html)对获得的发育树进一步编辑和美化(Xie et al.,2023),及对蛋白保守基序结果进行可视化。
使用STRING数据库(https://string-db.org/)对岩白菜TCP基因家族成员的蛋白质序列进行互作蛋白预测,物种参数选择模式植物拟南芥,阈值为0.4。
基于岩白菜转录组数据(Zhang et al.,2023),使用RSEM(http://deweylab.github.io/RSEM/)计算基因表达水平,并将单个基因的表达水平转换为TPM(转录本/百万)值。使用TBtools(Chen et al.,2020)软件绘制表达模式热图,表达值TPM进行了log2处理。
摘取对照组和低温胁迫组(处理温度:4°C,处理时间:6小时)的岩白菜顶端第1枚完全展开的叶片,转移至样品管中,使用多糖多酚植物RNA提取试剂盒(擎科生物,中国)提取RNA,随后使用反转录试剂盒(艾科瑞生物,中国)将RNA反转录为cDNA。随机选取6个BpTCP基因进行qRT-PCR验证。以18S rRNA为内参基因,实验所用引物采用Primer Premier 5.0软件设计(引物信息见附表1)。相对表达水平采用2–ΔΔCT法(Livak and Schmittgen,2001)计算。
基于课题组前期工作中获得的代谢组学数据(Zhu et al.,2024),鉴定出根、茎和叶中含量变化最大的20个次级代谢物,并使用R 4.0.2软件对BpTCP基因家族表达量与代谢物含量进行pearson相关性分析,利用在线软件tvbot对结果可视化。
基于岩白菜转录组测序数据,将含有完整TCP结构域的基因作为纳入BpTCP家族的基本标准,共鉴定出16个BpTCP基因,分别命名为BpTCP1–BpTCP16。对BpTCP蛋白的理化性质进行预测分析(表1),结果显示,BpTCP蛋白的肽长度介于177–553 aa之间,等电点(isoelectric point,PI)范围为5.45–9.71,蛋白质分子量范围为19247.83–58720.35 Da,所有BpT-CP蛋白的亲水性平均值都是负值,说明均为亲水性蛋白。亚细胞定位预测表明,BpTCP蛋白均位于细胞核,这与TCP转录因子主要在细胞核中发挥作用一致。
为了分析岩白菜TCP基因家族的进化关系,利用DNAMAN 9.0软件对拟南芥24个AtTCP基因、水稻22个OsTCP基因和本研究中鉴定到的岩白菜16个BpTCP基因进行多序列比对,并在MEGA7.0中通过邻接法构建系统发育树(图1)。根据系统进化树的拓扑结构,岩白菜TCP基因家族成员可以分为两大类:Class I和Class II。Class I亦称PCF类,包含12个BpTCP成员。Class II包含4个BpTCP成员,且这4个成员均属于CIN亚类。这一分类结果为理解BpTCP基因家族的进化关系和功能分化提供了重要线索。
基因结构的多样性促进了基因家族的进化。为深入探讨TCP基因家族的进化过程,我们结合系统进化树,利用MEME工具分析了BpTCP蛋白中存在的保守基序,共鉴定出10个不同的motif(图2A)。结果显示,Class I类的BpTCP蛋白成员普遍包含更多的保守基序,而Class II类BpTCP成员含有的保守基序相对较少。同时,同一组或亚组中的BpTCP含有相似的保守基序。例如,motif 3、motif 6、motif 7、motif 9和motif 10只分布在PCF亚族成员中。说明这些保守基序可能在基因进化和功能中发挥不同的作用。此外,所有BpTCP成员均含有保守的TCP结构域(motif 1),负责结合DNA。
为探究岩白菜TCP基因家族成员之间的互作关系,利用STRING在线软件构建了1个蛋白质互作网络(图2B),以模式植物拟南芥为参考物种。结果显示,鉴定的10个BpTCP蛋白之间存在28种相互作用,其中BpTCP4、BpTCP9、BpTCP10、BpTCP14以及BpTCP16展示出较高的互作连接性,形成一个关键的调控中心,可能在与BpTCPs相关的各种生物学过程中发挥关键作用。
为探究BpTCP基因在岩白菜不同组织中的表达模式,对岩白菜根、茎和叶的转录组数据进行分析,并利用TBtools软件制作表达热图(图3A)。结果表明,一些基因在3种组织中均保持高水平表达,如BpTCP7和BpTCP12,暗示它们可能在岩白菜生长发育中发挥作用。而大部分BpTCP基因在不同组织中的表达水平存在差异。例如,BpTCP1、BpTCP10和BpTCP4在叶片中的表达水平高于根和茎;BpTCP3主要在根和茎中表达;BpTCP5主要在叶和茎中表达。上述结果表明,BpTCP基因在岩白菜不同组织中行使不同功能。
为探讨BpTCP基因在低温胁迫响应中的作用,基于转录组数据对低温胁迫前后岩白菜叶片中BpTCP基因的表达变化进行分析并绘制热图(图3B)。结果显示,大部分BpTCP基因在低温胁迫下的表达水平未发生明显变化,表明这些基因在低温胁迫响应中的作用可能较小。而BpTCP10的表达水平在低温胁迫下明显上调,BpTCP1和BpTCP12在低温胁迫下的表达显著下调,暗示它们可能在岩白菜的耐寒性中发挥重要作用。为验证转录组数据的可靠性,我们挑选了6个BpTCP基因进行qRT-PCR验证,包括3个上调基因(BpTCP6、BpTCP7和BpTCP10)以及3个下调基因(BpTCP1、BpTCP12和BpTCP16)。结果显示,这6个BpTCP基因的表达趋势与转录组测序结果基本一致(图4)。
为探讨BpTCP基因家族在岩白菜次级代谢物合成路径中的调控作用,本研究基于转录组数据和代谢组数据进行了BpTCP基因表达与次级代谢产物的关联分析,筛选并挖掘出与岩白菜次级代谢产物合成显著相关的BpTCP基因家族成员,结果如图5所示。
结果显示,BpTCP基因家族与许多代谢物表现出显著相关性。例如,原儿茶醛(3,4-dihydroxybenzal-dehyde)是一种重要的酚类化合物,已被证明具有抗炎和抗氧化等多种药理作用(Zhang et al.,2021)。原儿茶醛含量与BpTCP3和BpTCP11的表达量呈显著正相关。一些黄酮类化合物,如芦丁(rutin)、槲皮素-3-O-新橙皮苷(quercetin-3-O-neohesperidoside)和忍冬苷(lonicerin)含量,与BpTCP8、BpTCP10、BpTCP1、BpTCP4、BpTCP9、BpTCP6和BpTCP2的表达量呈极显著正相关。这些黄酮类化合物因具抗炎、抗氧化和抗癌特性,成为各种营养保健品、药品和化妆品中不可或缺的组成部分(Panche et al.,2016)。这一结果提示,这些基因可能在黄酮类化合物的代谢途径中发挥重要调控作用。此外,我们还分析了岩白菜素(bergenin)含量与BpTCP基因表达量的相关性。岩白菜素是岩白菜的主要生物活性成分之一,因最早从岩白菜中提取而得名。岩白菜素属于异香豆素类化合物,具有提高免疫、抗氧化、抗炎和抗糖尿病等作用,药用价值极高(Yan et al.,2024)。分析结果显示,BpTCP3、BpTCP16和BpTCP11表达与岩白菜素含量呈显著正相关,表明在这些基因表达量较高的组织中,岩白菜素的含量也相对较高。这一正相关性提示这些BpTCP基因可能在岩白菜素的合成或积累过程中发挥促进作用。
TCP基因家族作为植物中重要的转录因子家族,在植物生长发育、应激反应和次生代谢等过程中发挥重要作用(Manassero et al.,2013)。目前,TCP基因家族已在多个物种中得到鉴定和研究,但在岩白菜中尚未见相关报道。本研究基于岩白菜转录组数据,通过筛选鉴定到16个BpTCP基因家族成员;并对其基本理化性质、亚细胞定位和系统进化关系等进行详细分析。理化性质分析结果表明,所有BpTCP蛋白均为亲水性蛋白,其中5个为碱性蛋白,其余为酸性蛋白。亚细胞定位预测结果表明,BpTCP蛋白均定位于细胞核,这与其它物种的TCP转录因子一致,主要在细胞核中发挥作用(Perez et al.,2019)。
系统进化分析结果显示,16个BpTCP基因可分为Class I和Class II两大分支。Class I包含12个BpTCP成员;Class II包含4个BpTCP成员,均属于CIN亚类。此前的研究发现,Class I类TCP基因通常参与调控细胞的增殖和生长,而Class II类TCP基因主要参与调控细胞分化和器官的形态建成(Viola and Gonzalez,2023)。例如,AtTCP4作为miR319a的关键靶点,对于拟南芥花瓣的形成和发育至关重要(Nag et al.,2009)。岩白菜中与AtTCP4同属于Class II类的4个BpTCP基因可能也具有类似的功能。蛋白保守基序分析结果显示,Class I类BpTCP蛋白包含的保守基序更多,表明其在进化过程中受到较强的纯化选择;而Class II类BpTCP成员含有的保守基序相对较少,可能经历了功能分化以适应不同的发育和环境需求。
通过对BpTCP基因家族的表达模式进行分析,可更深入地探究这些基因的功能。研究表明,拟南芥的5个CIN亚类基因AtTCP2、AtTCP3、AtTCP4、AtTCP5和AtTCP10在叶中高表达,并参与调控叶片发育(Palatnik et al.,2003;Ori et al.,2007)。本研究中,CIN亚类基因BpTCP1和BpTCP10在岩白菜叶片中高表达,推测它们可能也具有调控叶片发育的作用。此外,还有研究表明TCP基因家族在低温胁迫响应过程中发挥重要作用。例如,过表达DgTCP1提高了菊花对低温胁迫的耐受性(Li et al.,2022);OsTCP19负调节水稻耐寒性(Li et al.,2025)。本研究进一步对BpTCP基因家族在低温胁迫下的表达模式进行分析,发现BpTCP10、BpTCP1和BpTCP12在低温胁迫下表达变化显著,表明这些基因可能在岩白菜的低温胁迫响应中发挥作用,是进一步探索岩白菜耐寒机制的关键候选基因。
在漫长的进化过程中,植物与其生存环境不断互作,根据初级生长的需求产生了多种类型的次级代谢物。在次生代谢方面,TCP基因家族同样发挥重要调控作用。有研究表明,黄花蒿(Artemisia annua)的AaTCP14和AaTCP15基因参与调节青蒿素的生物合成(Ma et al.,2021);拟南芥的AtTCP3基因通过与R2R3-MYB蛋白互作,增强类黄酮的生物合成(Li and Zachgo,2013)。岩白菜作为一种重要的药用植物,富含多种次级代谢物(如黄酮类和酚酸类化合物),这些成分赋予了岩白菜抗氧化和抗炎等多种药理活性(Zhang et al.,2011)。本研究发现,BpTCP8、BpTCP10和BpTCP1等基因的表达与槲皮素-3-O-新橙皮苷以及芦丁等黄酮类物质的含量呈显著正相关;BpTCP3、BpTCP16和BpTCP11的表达与岩白菜素的含量显著正相关。上述结果表明,BpTCP基因家族可能参与调控岩白菜的次生代谢过程,为进一步研究BpTCP基因的功能提供了重要线索。

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doi: 10.11983/CBB25008
  • 接收时间:2025-01-16
  • 首发时间:2026-10-15
  • 出版时间:2026-01-10
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  • 收稿日期:2025-01-16
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    1西南交通大学生命科学与工程学院,成都 610031
    2四川省成都市石室中学,成都 610041

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2种不同金属材料的力学参数
科
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属数
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genus
种数
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species
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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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