Article(id=1304414807524922275, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414798482010221, articleNumber=null, orderNo=null, doi=10.7501/j.issn.0253-2670.2026.05.021, pmid=null, cstr=null, oa=null, hot=0, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1759334400000, receivedDateStr=2025-10-02, revisedDate=null, revisedDateStr=null, acceptedDate=null, acceptedDateStr=null, onlineDate=1788926324969, onlineDateStr=2026-09-09, pubDate=null, pubDateStr=null, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1788926324969, onlineIssueDateStr=2026-09-09, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1788926324969, creator=13701087609, updateTime=1788926324969, updator=13701087609, issue=Issue{id=1304414798482010221, tenantId=1146029695717560320, journalId=1302319053441957962, year='2026', volume='57', issue='5', pageStart='1597', pageEnd='2008', issueExtLink='null', onlineDate='null', pubDate='1773244800000', pubDateStr='2026-03-12', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1788926322813, creator='13701087609', updateTime=1788926625459, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1304416067925864795, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414798482010221, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1304416067925864796, tenantId=1146029695717560320, journalId=1302319053441957962, issueId=1304414798482010221, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=1841, endPage=1852, ext={EN=ArticleExt(id=1304414808275702693, articleId=1304414807524922275, tenantId=1146029695717560320, journalId=1302319053441957962, language=EN, title=Genome-wide identification and expression analysis of PKS III gene family in Polygonum cuspidatum, columnId=null, journalTitle=Chinese Traditional and Herbal Drugs, columnName=null, runingTitle=null, highlight=null, articleAbstract=Objective To identify the genome-wide family members of type III polyketide synthase (PKS III) and conduct bioinformatics analysis and expression profile analysis and clarify the relationship between their expression and the content of active components of Huzhang (Polygonum cuspidatum). Methods Based on the genome data of P. cuspidatum, the members of PKS III gene family were identified. Subsequently, the characteristics of these members were analyzed, including the physicochemical properties of their encoded proteins, secondary structure, phylogeny, and conserved motifs. Transcriptome data were further used to analyze their expression profiles, and the correlation between the expression levels of these PKS III genes and the active components was investigated. Results A total of 73 PKS III members were identified in the whole genome of P. cuspidatum, which were unevenly distributed on 20 chromosomes. Subcellular localization prediction indicated that most PKS III members were localized in the cytoplasm, while a small portion were localized on the plasma membrane. Phylogenetic analysis revealed that they were clustered into three major groups, and members within the same group shared identical conserved domains. Analysis of promoter cis-acting elements demonstrated that the PKS III genes contained various elements responsive to hormones, light, and growth and development. Expression profile analysis showed significant differences in the expression of PKS III genes among five tissues of roots and rhizomes of P. cuspidatum. Specifically, the expression levels of PKS32 and PKS42 were significantly higher than those of other genes in all tissues, with the highest expression detected in the rhizome pith. Correlation analysis indicated that PKS3, PKS8, PKS21, PKS44, PKS58, and PKS61 exhibited a significant positive correlation with the contents of polydatin and physcion, and PKS27, PKS56, and PKS69 showed a significant positive correlation with the contents of resveratrol and emodin; and PKS32 and PKS42 displayed a significant positive correlation with the content of physcion. Conclusion A total of 73 PKS III family members were identified, and the expression levels of some members correlated significantly with the contents of active components in P. cuspidatum roots and rhizomes. This study provides a foundation for subsequent research on the functions of PKS III genes and for elucidating the biosynthetic mechanisms of anthraquinones, stilbenes, and flavonoids in P. cuspidatum., authors=HU Die, CHEN Lina, ZHANG Yunting, CHEN Qingmei, LUO Chao, DENG Aiping, YU Kun, authorsList=HU Die, CHEN Lina, ZHANG Yunting, CHEN Qingmei, LUO Chao, DENG Aiping, YU Kun, authorCompany=null, correspAuthors=null, 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=1304414807969518500, articleId=1304414807524922275, tenantId=1146029695717560320, journalId=1302319053441957962, language=CN, title=虎杖PKS III基因家族全基因组鉴定及表达分析, columnId=1304140203967410414, journalTitle=中草药, columnName=药材与资源, runingTitle=null, highlight=null, articleAbstract=目的 鉴定虎杖Polygonum cuspidatum PKS III基因组家族成员，对其进行生物信息学分析、表达特征分析，并明确其表达量与虎杖药材有效成分含量的关系。方法 依据虎杖基因组数据，鉴定虎杖PKS III基因家族成员，分析其蛋白理化性质、二级结构、系统发育和保守基序等特征，利用转录组数据分析其表达特征，研究表达量与药材有效成分相关性。结果 虎杖全基因组中共鉴定出73个PKS III成员，不均匀地分布在20条染色体上；亚细胞定位预测显示，大部分PKS III定位于细胞质中，小部分定位于质膜上。系统发育分析表明，73个PKS III被分为3大类，同一类中的PKS III拥有相同的保守结构域。通过启动子顺式作用元件分析，虎杖PKS III基因具有多种激素响应、光响应和生长发育响应元件。表达特征分析显示，PKS III基因在虎杖药材根及根茎的5个组织中存在较大表达差异，PKS32、PKS42在所有组织中的表达量均显著高于其他基因，在根茎髓部表达量最高；相关性分析发现PKS3、PKS8、PKS21、PKS44、PKS58、PKS61与虎杖苷、大黄素甲醚含量呈显著正相关；PKS27、PKS56、PKS69与白藜芦醇和大黄素含量呈显著正相关；PKS32和PKS42与大黄素甲醚含量呈显著正相关。结论 鉴别出73个虎杖PKS III家族成员，部分成员基因表达量与虎杖药材有效成分含量具有显著相关性，为后续研究虎杖PKS III基因功能、阐明虎杖蒽醌类、二苯乙烯类及黄酮类成分的生物合成机制提供基础。, authors=胡碟1, 陈丽娜1, 张云婷1, 陈庆梅2, 罗超3, 邓爱平1, 余坤1,4, authorsList=胡碟, 陈丽娜, 张云婷, 陈庆梅, 罗超, 邓爱平, 余坤, authorCompany=1 湖北中医药大学药学院, 湖北 武汉 430070; 2 湖北省中医院, 湖北 武汉 430061; 3 湖北福人药业股份有限公司, 湖北 通城 437400; 4 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Combinatorial approaches to polyketide biosynthesis[J]. Curr Opin Chem Biol, 1997, 1(2): 162-168. Guo D M, Wang H Y, Zhang S M, et al. The type III polyketide synthase supergene family in plants: Complex evolutionary history and functional divergence[J]. Plant J, 2022, 112(2): 414-428. Funa N, Ohnishi Y, Fujii I, et al. A new pathway for polyketide synthesis in microorganisms[J]. Nature, 1999, 400(6747): 897-899. 王彬彬, 魏建和, 宋振巧, 等. 植物III型聚酮合酶研究进展[J]. 中国中药杂志, 2018, 43(13): 2639-2647. Hu L F, He H H, Zhu C L, et al. Genome-wide identification and phylogenetic analysis of the Chalcone synthase gene family in rice[J]. J Plant Res, 2017, 130(1): 95-105. 马兰青, 师光禄, 叶和春, 等. 植物类型III聚酮合酶超家族基因结构、功能及代谢产物[J]. 生物工程学报, 2010, 26(11): 1482-1492. Schröder J. A family of plant-specific polyketide synthases: Facts and predictions[J]. Trends Plant Sci, 1997, 2(10): 373-378. 侯淇允, 张林林, 郝艳琦, 等. 虎杖研究进展及质量标志物预测[J]. 中国现代中药, 2024, 26(5): 912-926. 时圣明, 潘明佳, 王文倩, 等. 虎杖的化学成分及药理作用研究进展[J]. 药物评价研究, 2016, 39(2): 313-317. 张云婷, 黄晓, 陈运中, 等. 虎杖主要化学成分及其生物合成机制研究进展[J]. 中国中药杂志, 2020, 45(18): 4364-4372. Guo Y W, Nassar S, Ma L Q, et al. Octaketide synthase from Polygonum cuspidatum implements emodin biosynthesis in Arabidopsis thaliana[J]. Plant Cell Physiol, 2021, 62(3): 424-435. 贺志敏, 马文瑞, 于丽平, 等. 定点突变提高虎杖聚酮合酶的苯亚甲基丙酮合酶活性[J]. 生物工程学报, 2023, 39(7): 2806-2817. 朱雪雯, 米要磊, 孟祥霄, 等. 汉麻聚酮合酶基因家族成员鉴定与表达分析[J]. 中草药, 2023, 54(3): 886-897. Pothiraj R, Ravikumar M J, Suthanthiram B, et al. Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism[J]. Gene, 2021, 778: 145472. Sharma A, Shahzad B, Rehman A, et al. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress[J]. Molecules, 2019, 24(13): 2452. Su S Y, Xuan X Y, Tan J Q, et al. Analysis of the CHS gene family reveals its functional responses to hormones, salinity, and drought stress in moso bamboo (Phyllostachys edulis)[J]. Plants, 2025, 14(2): 161. Zhang Y H, Zheng L L, Zheng Y, et al. Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum[J]. Front Plant Sci, 2019, 10: 1274. 何梦媛, 姚华, 李国治, 等. 甘草CHS基因家族鉴定、表达特性分析及其与甘草查尔酮A积累的关系研究[J]. 植物生理学报, 2022, 58(1): 141-154. 赖恭梯, 阙秋霞, 潘若, 等. 刺葡萄查尔酮合成酶基因CHS对不同光质的响应及转录因子调控分析[J]. 生物技术通报, 2022, 38(11): 129-139. Wang Z B, Yu Q B, Shen W X, et al. Functional study of CHS gene family members in Citrus revealed a novel CHS gene affecting the production of flavonoids[J]. BMC Plant Biol, 2018, 18(1): 189. Wang Y Y, Xiao Y Q, Sun Y T, et al. Two B-box proteins, PavBBX6/9, positively regulate light-induced anthocyanin accumulation in sweet cherry[J]. Plant Physiol, 2023, 192(3): 2030-2048. 梁春晓, 王珊珊, 陈淑静, 等. 虎杖化学成分及药理活性研究进展[J]. 中草药, 2022, 53(4): 1264-1276. 万丽云, 任伟芳, 王斯健, 等. 花生白藜芦醇和查尔酮合成酶基因的鉴定与表达分析[J]. 中国油料作物学报, 2023, 45(1): 102-110. Xie Z W, Yang L, Fan M, et al. Genome-wide identification, characterization and expression analysis of the Chalcone synthase gene family in Chinese cabbage[J]. BMC Genomics, 2025, 26(1): 168.)
Objective To identify the genome-wide family members of type III polyketide synthase (PKS III) and conduct bioinformatics analysis and expression profile analysis and clarify the relationship between their expression and the content of active components of Huzhang (Polygonum cuspidatum). Methods Based on the genome data of P. cuspidatum, the members of PKS III gene family were identified. Subsequently, the characteristics of these members were analyzed, including the physicochemical properties of their encoded proteins, secondary structure, phylogeny, and conserved motifs. Transcriptome data were further used to analyze their expression profiles, and the correlation between the expression levels of these PKS III genes and the active components was investigated. Results A total of 73 PKS III members were identified in the whole genome of P. cuspidatum, which were unevenly distributed on 20 chromosomes. Subcellular localization prediction indicated that most PKS III members were localized in the cytoplasm, while a small portion were localized on the plasma membrane. Phylogenetic analysis revealed that they were clustered into three major groups, and members within the same group shared identical conserved domains. Analysis of promoter cis-acting elements demonstrated that the PKS III genes contained various elements responsive to hormones, light, and growth and development. Expression profile analysis showed significant differences in the expression of PKS III genes among five tissues of roots and rhizomes of P. cuspidatum. Specifically, the expression levels of PKS32 and PKS42 were significantly higher than those of other genes in all tissues, with the highest expression detected in the rhizome pith. Correlation analysis indicated that PKS3, PKS8, PKS21, PKS44, PKS58, and PKS61 exhibited a significant positive correlation with the contents of polydatin and physcion, and PKS27, PKS56, and PKS69 showed a significant positive correlation with the contents of resveratrol and emodin; and PKS32 and PKS42 displayed a significant positive correlation with the content of physcion. Conclusion A total of 73 PKS III family members were identified, and the expression levels of some members correlated significantly with the contents of active components in P. cuspidatum roots and rhizomes. This study provides a foundation for subsequent research on the functions of PKS III genes and for elucidating the biosynthetic mechanisms of anthraquinones, stilbenes, and flavonoids in P. cuspidatum.
HU Die, CHEN Lina, ZHANG Yunting, CHEN Qingmei, LUO Chao, DENG Aiping, YU Kun.
Genome-wide identification and expression analysis of PKS III gene family in Polygonum cuspidatum[J].
Chinese Traditional and Herbal Drugs,
2026
, 57
(5)
: 1841
-1852
.
DOI: 10.7501/j.issn.0253-2670.2026.05.021
Leadlay P F. Combinatorial approaches to polyketide biosynthesis[J]. Curr Opin Chem Biol, 1997, 1(2): 162-168. Guo D M, Wang H Y, Zhang S M, et al. The type III polyketide synthase supergene family in plants: Complex evolutionary history and functional divergence[J]. Plant J, 2022, 112(2): 414-428. Funa N, Ohnishi Y, Fujii I, et al. A new pathway for polyketide synthesis in microorganisms[J]. Nature, 1999, 400(6747): 897-899. 王彬彬, 魏建和, 宋振巧, 等. 植物III型聚酮合酶研究进展[J]. 中国中药杂志, 2018, 43(13): 2639-2647. Hu L F, He H H, Zhu C L, et al. Genome-wide identification and phylogenetic analysis of the Chalcone synthase gene family in rice[J]. J Plant Res, 2017, 130(1): 95-105. 马兰青, 师光禄, 叶和春, 等. 植物类型III聚酮合酶超家族基因结构、功能及代谢产物[J]. 生物工程学报, 2010, 26(11): 1482-1492. Schröder J. A family of plant-specific polyketide synthases: Facts and predictions[J]. Trends Plant Sci, 1997, 2(10): 373-378. 侯淇允, 张林林, 郝艳琦, 等. 虎杖研究进展及质量标志物预测[J]. 中国现代中药, 2024, 26(5): 912-926. 时圣明, 潘明佳, 王文倩, 等. 虎杖的化学成分及药理作用研究进展[J]. 药物评价研究, 2016, 39(2): 313-317. 张云婷, 黄晓, 陈运中, 等. 虎杖主要化学成分及其生物合成机制研究进展[J]. 中国中药杂志, 2020, 45(18): 4364-4372. Guo Y W, Nassar S, Ma L Q, et al. Octaketide synthase from Polygonum cuspidatum implements emodin biosynthesis in Arabidopsis thaliana[J]. Plant Cell Physiol, 2021, 62(3): 424-435. 贺志敏, 马文瑞, 于丽平, 等. 定点突变提高虎杖聚酮合酶的苯亚甲基丙酮合酶活性[J]. 生物工程学报, 2023, 39(7): 2806-2817. 朱雪雯, 米要磊, 孟祥霄, 等. 汉麻聚酮合酶基因家族成员鉴定与表达分析[J]. 中草药, 2023, 54(3): 886-897. Pothiraj R, Ravikumar M J, Suthanthiram B, et al. Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism[J]. Gene, 2021, 778: 145472. Sharma A, Shahzad B, Rehman A, et al. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress[J]. Molecules, 2019, 24(13): 2452. Su S Y, Xuan X Y, Tan J Q, et al. Analysis of the CHS gene family reveals its functional responses to hormones, salinity, and drought stress in moso bamboo (Phyllostachys edulis)[J]. Plants, 2025, 14(2): 161. Zhang Y H, Zheng L L, Zheng Y, et al. Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum[J]. Front Plant Sci, 2019, 10: 1274. 何梦媛, 姚华, 李国治, 等. 甘草CHS基因家族鉴定、表达特性分析及其与甘草查尔酮A积累的关系研究[J]. 植物生理学报, 2022, 58(1): 141-154. 赖恭梯, 阙秋霞, 潘若, 等. 刺葡萄查尔酮合成酶基因CHS对不同光质的响应及转录因子调控分析[J]. 生物技术通报, 2022, 38(11): 129-139. Wang Z B, Yu Q B, Shen W X, et al. Functional study of CHS gene family members in Citrus revealed a novel CHS gene affecting the production of flavonoids[J]. BMC Plant Biol, 2018, 18(1): 189. Wang Y Y, Xiao Y Q, Sun Y T, et al. Two B-box proteins, PavBBX6/9, positively regulate light-induced anthocyanin accumulation in sweet cherry[J]. Plant Physiol, 2023, 192(3): 2030-2048. 梁春晓, 王珊珊, 陈淑静, 等. 虎杖化学成分及药理活性研究进展[J]. 中草药, 2022, 53(4): 1264-1276. 万丽云, 任伟芳, 王斯健, 等. 花生白藜芦醇和查尔酮合成酶基因的鉴定与表达分析[J]. 中国油料作物学报, 2023, 45(1): 102-110. Xie Z W, Yang L, Fan M, et al. Genome-wide identification, characterization and expression analysis of the Chalcone synthase gene family in Chinese cabbage[J]. BMC Genomics, 2025, 26(1): 168.
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