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Article(id=1276531563684819100, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276531538535781212, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2025.04.005, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1732550400000, receivedDateStr=2024-11-26, revisedDate=null, revisedDateStr=null, acceptedDate=1733155200000, acceptedDateStr=2024-12-03, onlineDate=1782278441591, onlineDateStr=2026-06-24, pubDate=1745510400000, pubDateStr=2025-04-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782278441591, onlineIssueDateStr=2026-06-24, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782278441591, creator=13701087609, updateTime=1782278441591, updator=13701087609, issue=Issue{id=1276531538535781212, tenantId=1146029695717560320, journalId=1235980609244409860, year='2025', volume='46', issue='4', pageStart='777', pageEnd='1024', issueExtLink='null', onlineDate='null', pubDate='1745510400000', pubDateStr='2025-04-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782278435595, creator='13701087609', updateTime=1782278607615, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1276532260098675208, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276531538535781212, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1276532260098675209, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276531538535781212, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=820, endPage=830, ext={EN=ArticleExt(id=1276531565576450206, articleId=1276531563684819100, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=MiRNAs Analysis of Aquilaria sinensis Vitro Roots with Stress Memory Characteristic, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

The total RNA of Aquilaria sinensis vitro roots was extracted using the EASYspin Plus Plant Rapid Extraction Kit after three consecutive generations of salt stress treatment, and sequenced using the HiSeq 2500 high- throughput sequencing platform, aiming at exploring the roles of miRNAs in the three generations of A. sinensis vitro roots under salt stress and the metabolic pathways that may be involved in the regulation, and providing references to reveal the mechanisms of A. sinensis. The miRNA expression profiles of the first, second and third generations were obtained by using the high-throughput sequencing platform and bioinformatics technology, and the differential miRNAs in the three generations of vitro roots were screened, and the target genes of the differential miRNAs were predicted, and then the target gene analysis was performed to obtain the miRNAs that might be involved in the secondary metabolites of A. sinensis and those that were related to the response to salt stress. The results showed that 508 known miRNAs and 764 new predicted miRNAs were detected in the first-generation samples; 444 known miRNAs and 673 new predicted miRNAs were detected in the second-generation samples; 904 known miRNAs and 1100 new predicted miRNAs were detected in the third-generation samples. A total of 59 differentially expressed miRNAs and 275 target genes were obtained from the three samples. The up-regulated miRNA target genes were mainly involved in flavonoid biosynthesis and glutathione metabolism, while the down-regulated miRNA target genes were mainly involved in phenylpropanoid biosynthesis, Plant hormone signal transduction, plant-pathogen interactions and other signaling pathways. The key miRNAs were selected for NR annotation, and it was found that miR8020-x and novel-m0628-5p might be involved in the synthesis of secondary metabolites in A. sinensis vitro roots, and miR7494-y, miR477-y, miR5185-y, miR7757-y, miR408-z, and novel-m0628-5p might be responded to A. sinensis vitro roots salt stress. In this study, we used high-throughput sequencing to obtain miRNA expression profiles of A. sinensis vitro roots under salt stress, and bioinformatics analysis to obtain miRNAs that may be involved in secondary metabolites of A. sinensis and those related to the response to salt stress. The results of the present study will help to enhance the understanding of the miRNA regulatory mechanisms of A. sinensis under salt stress conditions and provide a new pathway for the synthesis of secondary metabolites of A. sinensis.

, authors=null, authorsList=Tingting ZHUANG, Jiaxin LI, Ruoting ZHAN, Xinye MA, authorCompany=null, correspAuthors=Xinye MA, 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=1276531567392583850, articleId=1276531563684819100, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=具胁迫“记忆”特征的白木香离体根的miRNA分析, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

本研究以白木香离体根为材料，在经过连续三代盐胁迫处理后，使用EASYspin Plus植物快速提取试剂盒提取样品的总RNA，利用HiSeq 2500高通量测序平台进行测序，旨在探讨miRNA在白木香三代离体根盐胁迫中发挥的作用及可能参与调控的代谢途径，为揭示白木香抵御盐胁迫机制的研究提供参考。取白木香三代盐胁迫的离体根为材料，通过使用高通量测序平台及生物信息学技术，获得第一代、第二代、第三代的miRNA表达谱，筛选三代离体根中的差异miRNA，对差异miRNA进行靶基因预测，之后进行靶基因分析，从而获得可能参与白木香次生代谢产物及响应盐胁迫相关的miRNA。结果显示：第一代样品中共检测出508个已知miRNA和764个新预测miRNA，第二代样品中共检测出444个已知miRNA和673个新预测miRNA，第三代样品中共检测出904个已知miRNA和1100个新预测miRNA。三代样品中共获得59个差异表达miRNA及275个靶基因，上调的miRNA靶基因主要参与类黄酮生物合成、谷胱甘肽代谢等信号通路，下调的miRNA靶基因则主要涉及苯丙烷类生物合成、植物激素信号传导、植物病原相互作用等信号通路。选取关键miRNA进行NR注释，结果发现，miR8020-x和novel-m0628-5p可能参与白木香离体根次生代谢产物合成；miR7494-y、miR477-y、miR5185-y、miR7757-y、miR408-z和novel-m0628-5p可能响应白木香离体根盐胁迫。本研究利用高通量测序得到白木香离体根盐胁迫的miRNA表达谱，并利用生物信息学分析得到可能参与白木香次生代谢产物及响应盐胁迫相关的miRNA，研究结果将有助于增强对白木香在盐胁迫条件下miRNA调控机制的认识，并为白木香次生代谢产物合成提供新的途径。

, authors=

庄婷婷（1998—），女，硕士研究生，研究方向：芳香药用植物资源学。

, authorsList=庄婷婷, 李佳欣, 詹若挺, 马新业, authorCompany=null, correspAuthors=马新业, authorNote=null, correspAuthorsNote=
* 马新业（MA Xinye），E-mail：。
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庄婷婷（1998—），女，硕士研究生，研究方向：芳香药用植物资源学。

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庄婷婷（1998—），女，硕士研究生，研究方向：芳香药用植物资源学。

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WANG P P, journalName=International Journal of Molecular Sciences, refType=null, unstructuredReference=ZHAO S S, ZHANG Q K, LIU M Y, ZHOU H P, MA C L, WANG P P. 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Cloning of glutathione peroxidase gene PeGPX from Populus euphratica and the salt tolerance of the transformed plants[J]. Genomics and Applied Biology, 2012, 31(3): 231-239. (in Chinese), articleTitle=Cloning of glutathione peroxidase gene PeGPX from Populus euphratica and the salt tolerance of the transformed plants, refAbstract=null), Reference(id=1276531580097130752, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2017, volume=18, issue=4, pageStart=818, pageEnd=null, url=null, language=null, rfNumber=[23], rfOrder=34, authorNames=JIA Q, XIAO Z X, WONG F L, SUN S, LIANG K J, LAM H M, journalName=Intemational Joumal of Molecular Sciences, refType=null, unstructuredReference=JIA Q, XIAO Z X, WONG F L, SUN S, LIANG K J, LAM H M. Genome-wide analyses of the soybeanf-box gene family in response to salt stress[J]. Intemational Joumal of Molecular Sciences, 2017, 18(4): 818., articleTitle=Genome-wide analyses of the soybeanf-box gene family in response to salt stress, refAbstract=null), Reference(id=1276531580168433921, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2017, volume=17, issue=1, pageStart=211, pageEnd=null, url=null, language=null, rfNumber=[24], rfOrder=35, authorNames=GUO Y, ZHAO S, ZHU C, CHANG X, YUE C, WANG Z, LIN Y, LAI Z, journalName=BMC Plant Biology, refType=null, unstructuredReference=GUO Y, ZHAO S, ZHU C, CHANG X, YUE C, WANG Z, LIN Y, LAI Z. Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress[J]. BMC Plant Biology, 2017, 17(1): 211., articleTitle=Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress, refAbstract=null), Reference(id=1276531580269097218, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2023, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[25], rfOrder=36, authorNames=赵婷, journalName=null, refType=null, unstructuredReference=赵婷. 不同穗发芽抗性小麦品种种子萌发过程中miRNAs的鉴定与比较分析[D]. 武汉: 华中农业大学, 2023., articleTitle=不同穗发芽抗性小麦品种种子萌发过程中miRNAs的鉴定与比较分析, refAbstract=null), Reference(id=1276531580332011779, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2023, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[25], rfOrder=37, authorNames=ZHANG T, journalName=null, refType=null, unstructuredReference=ZHANG T. Identification and comparative analysis of miRNAs during seed germination of wheat varieties with different pre-harvest sprouting resistance[D]. Wuhan: Huazhong Agricultural University, 2023. (in Chinese), articleTitle=Identification and comparative analysis of miRNAs during seed germination of wheat varieties with different pre-harvest sprouting resistance, refAbstract=null), Reference(id=1276531580399120644, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2015, volume=84, issue=1, pageStart=169, pageEnd=87, url=null, language=null, rfNumber=[26], rfOrder=38, authorNames=MA C, BURD S, LERS A, journalName=Plant Journal, refType=null, unstructuredReference=MA C, BURD S, LERS A. miR408 is involved in abioticstress responses in Arabidopsis[J]. Plant Journal, 2015, 84(1): 169-87., articleTitle=miR408 is involved in abioticstress responses in Arabidopsis, refAbstract=null), Reference(id=1276531580462035205, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2022, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[27], rfOrder=39, authorNames=战明慧, journalName=null, refType=null, unstructuredReference=战明慧. 苹果LysM类受体激酶基因MdLYK15对腐皮镰孢菌的响应和表达调控研究[D]. 杨凌: 西北农林科技大学, 2022. (in Chinese), articleTitle=苹果LysM类受体激酶基因MdLYK15对腐皮镰孢菌的响应和表达调控研究, refAbstract=null), Reference(id=1276531580524949766, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2022, volume=null, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[27], rfOrder=40, authorNames=ZHAN M H, journalName=null, refType=null, unstructuredReference=ZHAN M H. Functional analysis and transcriptional regulation of apple LysM receptor-like kinase gene MdLYK15 in response to Fusarium solani[D]. Yangling: Northwest Agriculture and Forestry University, 2022. (in Chinese), articleTitle=Functional analysis and transcriptional regulation of apple LysM receptor-like kinase gene MdLYK15 in response to Fusarium solani, refAbstract=null), Reference(id=1276531580608835847, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, doi=null, pmid=null, pmcid=null, year=2022, volume=60, issue=4, pageStart=1205, pageEnd=1221, url=null, language=null, rfNumber=[28], rfOrder=41, authorNames=LI Y, WANG L, YU B, GUO J, ZHAO Y, ZHU Y, journalName=Biochemical Genetics, refType=null, unstructuredReference=LI Y, WANG L, YU B, GUO J, ZHAO Y, ZHU Y. Expression analysis of AUX/IAA family genes in apple under salt stress[J]. Biochemical Genetics, 2022, 60(4): 1205-1221., articleTitle=Expression analysis of AUX/IAA family genes in apple under salt stress, refAbstract=null)], funds=[Fund(id=1276531575789580509, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, awardId=2023KJ148, language=CN, fundingSource=广东省乡村振兴战略专项-农业科技发展及资源环境保护管理项目-广东省现代南药产业技术体系创新团队项目(2023KJ148), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1276531567749099692, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, xref=null, ext=[AuthorCompanyExt(id=1276531567757488301, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, companyId=1276531567749099692, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=School of Chinese Materia Medica, Guangzhou University of Chinese Medicine / Ministry of Education Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education / National Engineering Research Center for Proprietary Chinese Medicines R&D Laboratory of Southern Medicines, Guangzhou, Guangdong 510006, China), AuthorCompanyExt(id=1276531567765876910, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, companyId=1276531567749099692, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=广州中医药大学中药学院/岭南中药资源教育部重点实验室/国家中成药工程技术研究中心南药研发实验室，广东广州　510006)])], figs=[ArticleFig(id=1276531572811624651, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Fig. 1, caption=Distribution of miRNA lengths under salt stress in A. sinensis vitro roots, figureFileSmall=RsMZtq75NpToJ4UpbI+rVA==, figureFileBig=hS3YNvPlwZpQC4VqOk2ikA==, tableContent=null), ArticleFig(id=1276531574443208908, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=图1, caption=白木香离体根盐胁迫下miRNA长度分布, figureFileSmall=RsMZtq75NpToJ4UpbI+rVA==, figureFileBig=hS3YNvPlwZpQC4VqOk2ikA==, tableContent=null), ArticleFig(id=1276531574644535501, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Fig. 2, caption=Known miRNAs and new predicted miRNAs identified under salt stress treatment in vitro roots, figureFileSmall=Y2yj9l91WCQObdIb2y84hQ==, figureFileBig=ewnnFNj+ldGeflitQhzfmQ==, tableContent=null), ArticleFig(id=1276531574703255758, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=图2, caption=离体根盐胁迫处理下鉴定的已知miRNA和新预测miRNA, figureFileSmall=Y2yj9l91WCQObdIb2y84hQ==, figureFileBig=ewnnFNj+ldGeflitQhzfmQ==, tableContent=null), ArticleFig(id=1276531574770364623, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Fig. 3, caption=Differentially expression analysis of miRNAs in three generations of A. sinensis vitro roots under salt stress, figureFileSmall=1K1gnzFUfXwZrCIooBSr9Q==, figureFileBig=XtsjoKRdWF7aM0IOcbbOaw==, tableContent=null), ArticleFig(id=1276531574824890576, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=图3, caption=盐胁迫下白木香三代离体根差异表达miRNA分析, figureFileSmall=1K1gnzFUfXwZrCIooBSr9Q==, figureFileBig=XtsjoKRdWF7aM0IOcbbOaw==, tableContent=null), ArticleFig(id=1276531574883610833, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Fig. 4, caption=GO functional annotation of differentially expressed miRNA target genes, figureFileSmall=yiieHk+0Hn263ISGxA0V9w==, figureFileBig=5nQb2xhplUmB6pieAJD3iw==, tableContent=null), ArticleFig(id=1276531574938136786, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=图4, caption=差异表达miRNA靶基因的GO功能注释, figureFileSmall=yiieHk+0Hn263ISGxA0V9w==, figureFileBig=5nQb2xhplUmB6pieAJD3iw==, tableContent=null), ArticleFig(id=1276531574996857043, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Fig. 5, caption=KEGG enrichment analysis of differentially expressed miRNA target genes, figureFileSmall=+HSrLuIwCAgoUhwz9sJBpA==, figureFileBig=MW1eMtSLU+6qCdPpGVm0XQ==, tableContent=null), ArticleFig(id=1276531575059771604, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=图5, caption=差异表达miRNA靶基因的KEGG富集分析, figureFileSmall=+HSrLuIwCAgoUhwz9sJBpA==, figureFileBig=MW1eMtSLU+6qCdPpGVm0XQ==, tableContent=null), ArticleFig(id=1276531575122686165, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Tab. 1, caption=

Sample data filtering statistics

, figureFileSmall=null, figureFileBig=null, tableContent=
编号No.高质量序列（占比）High_quality (ratio/%)无3'端接头的序列(占比)3' adapter_null (ratio/%)含5'端接头的序列5'（占比）adapter_contaminants (ratio/%)小于18 bp的序列（占比）Smaller_than_18nt (ratio/%)纯净序列（占比）Clean_tags (ratio/%)
G1-113 656 935（98.6）38 554（0.3）16 429（0.1）685 384（5.0）12 828 377（93.9）
G1-213 521 873（98.7）30 420（0.2）33 828（0.3）1 258 681（9.3）11 760 730（87.0）
G1-314 737 562（98.8）27 486（0.2）41 657（0.3）955 116（6.5）13 336 291（90.5）
G2-110 209 976（99.2）4 438（0.4）22 864（0.2）398 519（4.0）9 512 104（93.2）
G2-213 304 295（98.6）15 190（0.1）17 331（0.1）734 884（5.5）12 472 052（94.0）
G2-311 186 638（99.4）27 872（0.2）95 341（0.9）1 267 715（11.3）9 548 798（85.4）
G3-115 764 705（98.7）24 510（0.2）24 522（0.2）1 419 687（9.0）14 217 036（90.2）
G3-215 340 433（98.7）23 005（0.2）38 022（0.2）1 829 675（11.9）13 346 541（87.0）
G3-311 642 970（99.3）15 248（0.1）28 321（0.2）1 043 192（9.0）10 499 617（90.2）
), ArticleFig(id=1276531575189795030, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=表1, caption=

样品数据过滤数据统计

, figureFileSmall=null, figureFileBig=null, tableContent=
编号No.高质量序列（占比）High_quality (ratio/%)无3'端接头的序列(占比)3' adapter_null (ratio/%)含5'端接头的序列5'（占比）adapter_contaminants (ratio/%)小于18 bp的序列（占比）Smaller_than_18nt (ratio/%)纯净序列（占比）Clean_tags (ratio/%)
G1-113 656 935（98.6）38 554（0.3）16 429（0.1）685 384（5.0）12 828 377（93.9）
G1-213 521 873（98.7）30 420（0.2）33 828（0.3）1 258 681（9.3）11 760 730（87.0）
G1-314 737 562（98.8）27 486（0.2）41 657（0.3）955 116（6.5）13 336 291（90.5）
G2-110 209 976（99.2）4 438（0.4）22 864（0.2）398 519（4.0）9 512 104（93.2）
G2-213 304 295（98.6）15 190（0.1）17 331（0.1）734 884（5.5）12 472 052（94.0）
G2-311 186 638（99.4）27 872（0.2）95 341（0.9）1 267 715（11.3）9 548 798（85.4）
G3-115 764 705（98.7）24 510（0.2）24 522（0.2）1 419 687（9.0）14 217 036（90.2）
G3-215 340 433（98.7）23 005（0.2）38 022（0.2）1 829 675（11.9）13 346 541（87.0）
G3-311 642 970（99.3）15 248（0.1）28 321（0.2）1 043 192（9.0）10 499 617（90.2）
), ArticleFig(id=1276531575256903895, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Tab. 2, caption=

Statistics of the top 10 known miRNAs and new predicted miRNAs expressed in samples

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miRNA长度Length/nt序列SequenceG1G2G3
miR166-y21TCGGACCAGGCTTCATTCCCC2 316 253.7693 947 914.1196 264 167.887
miR396-x21TTCCACAGCTTTCTTGAACTG675 094.1161 217 643.2131 892 737.329
miR156-x21TTGACAGAAGATAGAGAGCAC283 127.753522 513.619805 641.373
miR157-x21TTGACAGAAGATAGAGAGCAC228 373.079417 354.525645 727.604
miR398-x21GGAGCGACCTGAGATCACATG123 522.997242 633.392366 156.389
miR408-x21CAGGGAAGAGACAGAGCATGG98 874.286177 519.784276 394.070
miR159-y21TTTGGATTGAAGGGAGCTCTA84 214.939143 643.680227 858.619
miR7122-x22TTAGACAGAGAAATCACGGTGG80 259.852138 766.818219 026.669
miR162-y21TCGATAAACCTCTGCATCCAG64 593.526112 598.561177 192.087
miR156-y21GCTCACTCTCTATCTGTCACC38 787.99073 348.811112 136.801
novel-m0109-3p21ACCGTGTTTCTCTGTTCGAAC12 675.6598037.96930 391.845
novel-m0497-3p21CATGTGCCCCTCTTCCCCATC11 044.5169688.187344.175
novel-m0108-3p20CCACCGTGTTTCTCTGTCTA6893.5904270.4128597.977
novel-m0109-5p22TCGAACAGAGAAATCACGGTTG5102.0046405.5317949.745
novel-m0224-3p22TTGTCCTTGCGCATGGTTCCTC3186.1413446.2861934.236
novel-m0105-3p22TCGAAGGGGATGGGAGGGATGG2156.1641989.688383.329
novel-m0106-3p22TCGAAGGGGATGGGAGGGATGG2156.1641989.688383.329
novel-m0611-5p21GGAATGTTGTCTGGTTCGATG1573.4241526.0253309.866
novel-m0213-5p21TCCCTCCATCGTACCAGCTTT886.1981156.272457.478
novel-m0317-5p21AGATATTGGCGTGCCTCAATC817.402848.4041045.881
), ArticleFig(id=1276531575344984280, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=表2, caption=

样品表达量前10的已知miRNA和新预测miRNA统计

, figureFileSmall=null, figureFileBig=null, tableContent=
miRNA长度Length/nt序列SequenceG1G2G3
miR166-y21TCGGACCAGGCTTCATTCCCC2 316 253.7693 947 914.1196 264 167.887
miR396-x21TTCCACAGCTTTCTTGAACTG675 094.1161 217 643.2131 892 737.329
miR156-x21TTGACAGAAGATAGAGAGCAC283 127.753522 513.619805 641.373
miR157-x21TTGACAGAAGATAGAGAGCAC228 373.079417 354.525645 727.604
miR398-x21GGAGCGACCTGAGATCACATG123 522.997242 633.392366 156.389
miR408-x21CAGGGAAGAGACAGAGCATGG98 874.286177 519.784276 394.070
miR159-y21TTTGGATTGAAGGGAGCTCTA84 214.939143 643.680227 858.619
miR7122-x22TTAGACAGAGAAATCACGGTGG80 259.852138 766.818219 026.669
miR162-y21TCGATAAACCTCTGCATCCAG64 593.526112 598.561177 192.087
miR156-y21GCTCACTCTCTATCTGTCACC38 787.99073 348.811112 136.801
novel-m0109-3p21ACCGTGTTTCTCTGTTCGAAC12 675.6598037.96930 391.845
novel-m0497-3p21CATGTGCCCCTCTTCCCCATC11 044.5169688.187344.175
novel-m0108-3p20CCACCGTGTTTCTCTGTCTA6893.5904270.4128597.977
novel-m0109-5p22TCGAACAGAGAAATCACGGTTG5102.0046405.5317949.745
novel-m0224-3p22TTGTCCTTGCGCATGGTTCCTC3186.1413446.2861934.236
novel-m0105-3p22TCGAAGGGGATGGGAGGGATGG2156.1641989.688383.329
novel-m0106-3p22TCGAAGGGGATGGGAGGGATGG2156.1641989.688383.329
novel-m0611-5p21GGAATGTTGTCTGGTTCGATG1573.4241526.0253309.866
novel-m0213-5p21TCCCTCCATCGTACCAGCTTT886.1981156.272457.478
novel-m0317-5p21AGATATTGGCGTGCCTCAATC817.402848.4041045.881
), ArticleFig(id=1276531575428870361, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Tab. 3, caption=

Top 10 up-regulated, down-regulated miRNAs with differential expression between groups

, figureFileSmall=null, figureFileBig=null, tableContent=
组Group上调miRNAUp-regulated miRNA差异倍数Fold changeP值P下调miRNADown-regulated miRNA差异倍数Fold changeP值P
G1 vs G2novel-m0001-5p11.397 7670.044 648novel-m0244-5p–11.800 9460.037 762
novel-m0271-3p–11.621 8150.039 966
G1 vs G3novel-m0141-5p10.711 5670.005 860novel-m0561-3p–11.631 1600.006 446
novel-m0098-3p10.434 3950.004 184novel-m0271-3p–11.621 8150.011 475
novel-m0226-3p9.779 4790.037 407novel-m0161-3p–10.997 9670.022 497
novel-m0065-3p7.466 8890.001 222novel-m0620-3p–10.867 1730.033 285
novel-m0308-3p3.919 2910.046 455novel-m0363-5p–10.806 7780.028 692
novel-m0308-5p3.436 4030.047 956novel-m0593-3p–10.570 2790.018 212
miR390-y3.360 2680.040 017miR7757-y–10.419 7880.041 477
novel-m0396-5p–7.516 0960.002 802
novel-m0591-5p–6.616 2410.002 381
novel-m0256-5p–6.374 0340.003 907
G2 vs G3novel-m0098-3p10.434 3950.000 858novel-m0628-5p–11.209 3290.012 424
novel-m0015-3p9.222 3520.026 771novel-mo099-5p–11.113 3690.037 838
novel-m0441-3p9.079 3510.043 641novel-m0561-3p–10.916 6660.018 517
miR7494-y9.075 8710.039 750novel-m0533-3p–10.238 2850.044 501
novel-m0320-3p5.261 9130.033 898novel-m0336-3p–10.085 3930.046 369
novel-m0321-3p5.261 9130.033 822novel-m0396-5p–6.720 5780.004 122
novel-m0238-5p4.956 8190.006 719novel-m0001-5p–6.532 6730.008 632
novel-m0065-3p4.696 5870.006 680novel-m0591-5p–6.268 2760.000 886
novel-m0652-5p4.402 0370.032 568miR5185-y–6.216 9850.045 925
novel-m0464-3p4.098 5030.043 383novel-m0256-5p–5.654 6930.002 052
), ArticleFig(id=1276531575508562138, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=表3, caption=

各组间差异表达量前10的miRNA

, figureFileSmall=null, figureFileBig=null, tableContent=
组Group上调miRNAUp-regulated miRNA差异倍数Fold changeP值P下调miRNADown-regulated miRNA差异倍数Fold changeP值P
G1 vs G2novel-m0001-5p11.397 7670.044 648novel-m0244-5p–11.800 9460.037 762
novel-m0271-3p–11.621 8150.039 966
G1 vs G3novel-m0141-5p10.711 5670.005 860novel-m0561-3p–11.631 1600.006 446
novel-m0098-3p10.434 3950.004 184novel-m0271-3p–11.621 8150.011 475
novel-m0226-3p9.779 4790.037 407novel-m0161-3p–10.997 9670.022 497
novel-m0065-3p7.466 8890.001 222novel-m0620-3p–10.867 1730.033 285
novel-m0308-3p3.919 2910.046 455novel-m0363-5p–10.806 7780.028 692
novel-m0308-5p3.436 4030.047 956novel-m0593-3p–10.570 2790.018 212
miR390-y3.360 2680.040 017miR7757-y–10.419 7880.041 477
novel-m0396-5p–7.516 0960.002 802
novel-m0591-5p–6.616 2410.002 381
novel-m0256-5p–6.374 0340.003 907
G2 vs G3novel-m0098-3p10.434 3950.000 858novel-m0628-5p–11.209 3290.012 424
novel-m0015-3p9.222 3520.026 771novel-mo099-5p–11.113 3690.037 838
novel-m0441-3p9.079 3510.043 641novel-m0561-3p–10.916 6660.018 517
miR7494-y9.075 8710.039 750novel-m0533-3p–10.238 2850.044 501
novel-m0320-3p5.261 9130.033 898novel-m0336-3p–10.085 3930.046 369
novel-m0321-3p5.261 9130.033 822novel-m0396-5p–6.720 5780.004 122
novel-m0238-5p4.956 8190.006 719novel-m0001-5p–6.532 6730.008 632
novel-m0065-3p4.696 5870.006 680novel-m0591-5p–6.268 2760.000 886
novel-m0652-5p4.402 0370.032 568miR5185-y–6.216 9850.045 925
novel-m0464-3p4.098 5030.043 383novel-m0256-5p–5.654 6930.002 052
), ArticleFig(id=1276531575596642523, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=EN, label=Tab. 4, caption=

Differential miRNA key pathways and NR annotation

, figureFileSmall=null, figureFileBig=null, tableContent=
序号No.通路编号ID通路名称Pathway name靶基因Target genesmiRNANR注释NR note
1ko00010糖酵解/糖异生成Glycolysis/Gluconeogenesisevm.model.Scaffold 1.84novel-m0628-5p醛糖-1-/葡萄糖-6-磷酸1-酰亚胺酶[黄麻]
Aldose 1-/Glucose-6-phosphate 1-epimerase [Corchorus capsularis]
2ko01100代谢途径Metabolic pathwaysevm.model.Scaffold 446.31miR8020-x查尔酮黄酮异构酶[桃]
chalcone flavonone isomerase [Prunus persica]
evm.model.Scaffold 139.25novel-m0628-5p预测：线粒体含CBS结构域的蛋白CBSX3[柑橘]
PREDICTED: CBS domain-containing proteinCBSX3, mitochondrial [Citrus sinensis]
3ko00943类黄酮生物合成flavonoid biosynthesisevm.model.Scaffold 446.31miR8020-x查尔酮黄酮异构酶[桃]
chalcone flavonone isomerase [Prunus persica]
4ko00940苯丙烷类生物合成Phenylpropanoid biosynthesisevm.model.Scaffold 167.8miR5185-y预测：过氧化物酶44[梅]
PREDICTED: peroxidase 44 [Prunus mume]
5ko00480谷胱甘肽代谢Glutathione metabolismevm.model.Scaffold 195.28miR7494-y预测：可能的谷胱甘肽过氧化物酶2[可可豆]
PREDICTED: probable glutathione peroxidase 2 [Theobroma cacao]
6ko03018RNA降解RNA degradationevm.model.Scaffold 216.1novel-m0098-3pRNA螺旋酶，ATP依赖性，SK12/DOB1蛋白同工酶4[可可豆]
RNA helicase, ATP-dependent, SK12/DOB1protein isoform 4 [Theobroma cacao]
evm.model.Scaffold 26.304novel-m0161-3p预测：可能的CCR4相关因子1同源物11[胡杨]
PREDICTED: probable CCR4-associated factor 1homolog 11 [Populus euphratica]
7ko04075植物激素信号传导Plant hormone signal transductionevm.model.Scaffold 1.585miR7494-y富亮氨酸受体样蛋白激酶家族蛋白[可可豆]
Leucine-rich receptor-like protein kinase family protein [Theobroma cacao]
evm.model.Scaffold 24.124miR7757-y生长因子B3家族蛋白/辅助因子AUX/IAA相关同工酶1[可可豆]
ranscriptional factor B3 family protein / auxinresponsive factor AUX/IAA-related isoform 1[Theobroma cacao]
evm.model.Scaffold 403.11miR408-z预测：类生长素反应蛋白IAA6[陆地棉]
PREDICTED: auxin-responsive proteinIAA6-like [Gossypium hirsutum]
evm.model.Scaffold 140.3miR5185-y含F-box/WD重复蛋白pof10[豆属]F-box/WD repeat-containing protein pof10[Glycine soja]
8ko04016MAPK信号通路-植物MAPK signaling pathway-plantevm.model.Scaffold 43.133novel-m0628-5p预测：有丝分裂原活化蛋白激酶激酶2同工酶X1[柑橘属植物]
PREDICTED: mitogen-activated protein kinase kinase 2 isoform X1 [Citrus sinensis]
9ko04144内吞作用Endocytosisevm.model.Scaffold 3.680novel-m0320-3pSEC7样蛋白[黄麻]
SEC7-like protein [Corchorus capsularis]
10ko04626植物-病原体相互作用Plant-pathogen interactionevm.model.Scaffold 8.140miR477-y预测：lysM结构域受体样激酶3[可可豆]
PREDICTED: lysM domain receptor-like kinase3 [Theobroma cacao]
), ArticleFig(id=1276531575667945692, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276531563684819100, language=CN, label=表4, caption=

差异miRNA靶基因关键通路和NR注释

, figureFileSmall=null, figureFileBig=null, tableContent=
序号No.通路编号ID通路名称Pathway name靶基因Target genesmiRNANR注释NR note
1ko00010糖酵解/糖异生成Glycolysis/Gluconeogenesisevm.model.Scaffold 1.84novel-m0628-5p醛糖-1-/葡萄糖-6-磷酸1-酰亚胺酶[黄麻]
Aldose 1-/Glucose-6-phosphate 1-epimerase [Corchorus capsularis]
2ko01100代谢途径Metabolic pathwaysevm.model.Scaffold 446.31miR8020-x查尔酮黄酮异构酶[桃]
chalcone flavonone isomerase [Prunus persica]
evm.model.Scaffold 139.25novel-m0628-5p预测：线粒体含CBS结构域的蛋白CBSX3[柑橘]
PREDICTED: CBS domain-containing proteinCBSX3, mitochondrial [Citrus sinensis]
3ko00943类黄酮生物合成flavonoid biosynthesisevm.model.Scaffold 446.31miR8020-x查尔酮黄酮异构酶[桃]
chalcone flavonone isomerase [Prunus persica]
4ko00940苯丙烷类生物合成Phenylpropanoid biosynthesisevm.model.Scaffold 167.8miR5185-y预测：过氧化物酶44[梅]
PREDICTED: peroxidase 44 [Prunus mume]
5ko00480谷胱甘肽代谢Glutathione metabolismevm.model.Scaffold 195.28miR7494-y预测：可能的谷胱甘肽过氧化物酶2[可可豆]
PREDICTED: probable glutathione peroxidase 2 [Theobroma cacao]
6ko03018RNA降解RNA degradationevm.model.Scaffold 216.1novel-m0098-3pRNA螺旋酶，ATP依赖性，SK12/DOB1蛋白同工酶4[可可豆]
RNA helicase, ATP-dependent, SK12/DOB1protein isoform 4 [Theobroma cacao]
evm.model.Scaffold 26.304novel-m0161-3p预测：可能的CCR4相关因子1同源物11[胡杨]
PREDICTED: probable CCR4-associated factor 1homolog 11 [Populus euphratica]
7ko04075植物激素信号传导Plant hormone signal transductionevm.model.Scaffold 1.585miR7494-y富亮氨酸受体样蛋白激酶家族蛋白[可可豆]
Leucine-rich receptor-like protein kinase family protein [Theobroma cacao]
evm.model.Scaffold 24.124miR7757-y生长因子B3家族蛋白/辅助因子AUX/IAA相关同工酶1[可可豆]
ranscriptional factor B3 family protein / auxinresponsive factor AUX/IAA-related isoform 1[Theobroma cacao]
evm.model.Scaffold 403.11miR408-z预测：类生长素反应蛋白IAA6[陆地棉]
PREDICTED: auxin-responsive proteinIAA6-like [Gossypium hirsutum]
evm.model.Scaffold 140.3miR5185-y含F-box/WD重复蛋白pof10[豆属]F-box/WD repeat-containing protein pof10[Glycine soja]
8ko04016MAPK信号通路-植物MAPK signaling pathway-plantevm.model.Scaffold 43.133novel-m0628-5p预测：有丝分裂原活化蛋白激酶激酶2同工酶X1[柑橘属植物]
PREDICTED: mitogen-activated protein kinase kinase 2 isoform X1 [Citrus sinensis]
9ko04144内吞作用Endocytosisevm.model.Scaffold 3.680novel-m0320-3pSEC7样蛋白[黄麻]
SEC7-like protein [Corchorus capsularis]
10ko04626植物-病原体相互作用Plant-pathogen interactionevm.model.Scaffold 8.140miR477-y预测：lysM结构域受体样激酶3[可可豆]
PREDICTED: lysM domain receptor-like kinase3 [Theobroma cacao]
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具胁迫“记忆”特征的白木香离体根的miRNA分析
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庄婷婷 , 李佳欣 , 詹若挺 , 马新业 *
热带作物学报 | 组学与生物技术 2025,46(4): 820-830
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热带作物学报 |组学与生物技术 2025 , 46 (4) : 820 -830
具胁迫“记忆”特征的白木香离体根的miRNA分析
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庄婷婷, 李佳欣, 詹若挺, 马新业*
作者信息
  • 广州中医药大学中药学院/岭南中药资源教育部重点实验室/国家中成药工程技术研究中心南药研发实验室，广东广州　510006
通讯作者:
* 马新业（MA Xinye），E-mail：。
MiRNAs Analysis of Aquilaria sinensis Vitro Roots with Stress Memory Characteristic
Tingting ZHUANG, Jiaxin LI, Ruoting ZHAN, Xinye MA*
Affiliations
  • School of Chinese Materia Medica, Guangzhou University of Chinese Medicine / Ministry of Education Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education / National Engineering Research Center for Proprietary Chinese Medicines R&D Laboratory of Southern Medicines, Guangzhou, Guangdong 510006, China
出版时间: 2025-04-25 doi: 10.3969/j.issn.1000-2561.2025.04.005
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摘要
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本研究以白木香离体根为材料，在经过连续三代盐胁迫处理后，使用EASYspin Plus植物快速提取试剂盒提取样品的总RNA，利用HiSeq 2500高通量测序平台进行测序，旨在探讨miRNA在白木香三代离体根盐胁迫中发挥的作用及可能参与调控的代谢途径，为揭示白木香抵御盐胁迫机制的研究提供参考。取白木香三代盐胁迫的离体根为材料，通过使用高通量测序平台及生物信息学技术，获得第一代、第二代、第三代的miRNA表达谱，筛选三代离体根中的差异miRNA，对差异miRNA进行靶基因预测，之后进行靶基因分析，从而获得可能参与白木香次生代谢产物及响应盐胁迫相关的miRNA。结果显示：第一代样品中共检测出508个已知miRNA和764个新预测miRNA，第二代样品中共检测出444个已知miRNA和673个新预测miRNA，第三代样品中共检测出904个已知miRNA和1100个新预测miRNA。三代样品中共获得59个差异表达miRNA及275个靶基因，上调的miRNA靶基因主要参与类黄酮生物合成、谷胱甘肽代谢等信号通路，下调的miRNA靶基因则主要涉及苯丙烷类生物合成、植物激素信号传导、植物病原相互作用等信号通路。选取关键miRNA进行NR注释，结果发现，miR8020-x和novel-m0628-5p可能参与白木香离体根次生代谢产物合成；miR7494-y、miR477-y、miR5185-y、miR7757-y、miR408-z和novel-m0628-5p可能响应白木香离体根盐胁迫。本研究利用高通量测序得到白木香离体根盐胁迫的miRNA表达谱，并利用生物信息学分析得到可能参与白木香次生代谢产物及响应盐胁迫相关的miRNA，研究结果将有助于增强对白木香在盐胁迫条件下miRNA调控机制的认识，并为白木香次生代谢产物合成提供新的途径。

白木香  /  胁迫记忆  /  miRNA  /  HiSeq 2500高通量测序

The total RNA of Aquilaria sinensis vitro roots was extracted using the EASYspin Plus Plant Rapid Extraction Kit after three consecutive generations of salt stress treatment, and sequenced using the HiSeq 2500 high- throughput sequencing platform, aiming at exploring the roles of miRNAs in the three generations of A. sinensis vitro roots under salt stress and the metabolic pathways that may be involved in the regulation, and providing references to reveal the mechanisms of A. sinensis. The miRNA expression profiles of the first, second and third generations were obtained by using the high-throughput sequencing platform and bioinformatics technology, and the differential miRNAs in the three generations of vitro roots were screened, and the target genes of the differential miRNAs were predicted, and then the target gene analysis was performed to obtain the miRNAs that might be involved in the secondary metabolites of A. sinensis and those that were related to the response to salt stress. The results showed that 508 known miRNAs and 764 new predicted miRNAs were detected in the first-generation samples; 444 known miRNAs and 673 new predicted miRNAs were detected in the second-generation samples; 904 known miRNAs and 1100 new predicted miRNAs were detected in the third-generation samples. A total of 59 differentially expressed miRNAs and 275 target genes were obtained from the three samples. The up-regulated miRNA target genes were mainly involved in flavonoid biosynthesis and glutathione metabolism, while the down-regulated miRNA target genes were mainly involved in phenylpropanoid biosynthesis, Plant hormone signal transduction, plant-pathogen interactions and other signaling pathways. The key miRNAs were selected for NR annotation, and it was found that miR8020-x and novel-m0628-5p might be involved in the synthesis of secondary metabolites in A. sinensis vitro roots, and miR7494-y, miR477-y, miR5185-y, miR7757-y, miR408-z, and novel-m0628-5p might be responded to A. sinensis vitro roots salt stress. In this study, we used high-throughput sequencing to obtain miRNA expression profiles of A. sinensis vitro roots under salt stress, and bioinformatics analysis to obtain miRNAs that may be involved in secondary metabolites of A. sinensis and those related to the response to salt stress. The results of the present study will help to enhance the understanding of the miRNA regulatory mechanisms of A. sinensis under salt stress conditions and provide a new pathway for the synthesis of secondary metabolites of A. sinensis.

Aquilaria sinensis  /  stress memory  /  miRNAs  /  HiSeq 2500 high-throughput sequencing
庄婷婷, 李佳欣, 詹若挺, 马新业. 具胁迫“记忆”特征的白木香离体根的miRNA分析. 热带作物学报, 2025 , 46 (4) : 820 -830 . DOI: 10.3969/j.issn.1000-2561.2025.04.005
Tingting ZHUANG, Jiaxin LI, Ruoting ZHAN, Xinye MA. MiRNAs Analysis of Aquilaria sinensis Vitro Roots with Stress Memory Characteristic[J]. Chinese Journal of Tropical Crops, 2025 , 46 (4) : 820 -830 . DOI: 10.3969/j.issn.1000-2561.2025.04.005
正文
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盐胁迫作为一种严重影响植物生长发育的环境胁迫，可引发植物体内产生离子和渗透胁迫，进而影响植物体内次生代谢产物的积累或减少[1-2]。多项研究表明，不同植物在应对盐胁迫时展现出独特的生理适应机制，如胡椒（Piper Nigrum）[3]、连钱草（Glechoma longtituba）[4]和杠柳（Periploca sepium Bunge）[5]在盐胁迫下某些次生代谢产物增加，而藏红花（Crocus sativus）[6]和荆芥（Schizonepeta tenuifolia）[7]中次生代谢产物则呈现出不同程度的减少。近年来的研究表明，MicroRNA（miRNA）在植物盐胁迫响应中起着关键作用，并通过转录后调控靶基因表达影响植物耐盐性及次生代谢物合成[8-9]。在拟南芥（Arabidopsis thaliana）中，MA等[10]发现miR171在盐胁迫下调控靶基因GRAS，通过改变植株根系miRNA的表达来提高植物的耐盐性。水稻（Oryza sativa）中，特定miRNA（miR1841）的过表达显著减轻了盐胁迫[11]。这些研究成果为深入理解植物在盐胁迫下的分子调控机制奠定基础。
白木香[Aquilaria sinensis（Lour.）Gilg]为瑞香科（Thymelaeaceae）沉香属（Aquilaria L.）常绿乔木，其含树脂心材沉香，具有极高的药用价值，同时也是名贵香料，在医药、香料等行业有着广泛应用[12]。然而，自然环境下，野生沉香属植物受损后通常需要数十年时间才能形成沉香木[13]，这极大地限制了沉香的供应，导致其市场需求与自然产出之间存在巨大差距。沉香木（结香）的形成是树体在环境胁迫下逐渐积累次生代谢物的过程，因此，许多研究者致力于寻找有效的诱导方法来加速沉香的形成。盐胁迫作为一种化学诱导手段逐渐受到重视，因其能够诱导白木香愈伤组织产生2-（2-苯乙基）色酮类化合物[14]，且白木香离体根在多代的盐胁迫下表现出“胁迫记忆”特征[15]，这表明着盐胁迫可能在白木香结香过程中扮演着重要角色。目前关于白木香中盐胁迫与miRNA的关系研究尚处于起步阶段。尤其是miRNA在盐胁迫下如何调控白木香次生代谢产物积累以促进结香的机制仍不清楚。鉴于此，本研究将对白木香三代离体根进行Small RNA测序，并结合生物信息学分析筛选出差异表达的miRNA及其靶基因。一方面，旨在揭示miRNA在白木香适应盐胁迫过程中的分子调控网络，为全面理解白木香抗逆机制提供关键依据；另一方面，通过分析与次生代谢产物相关的miRNA，探索其在促进白木香结香相关次生代谢过程中的潜在作用。尽管目前尚未有直接证据表明盐胁迫下白木香的结香时间、产量或质量会发生改变，但本研究有望为后续研究提供重要线索，从而为推动白木香抗逆性研究及促进沉香产业的可持续发展提供理论支撑和新的研究思路。
1　材料与方法
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1.1　材料
1.1.1　植物材料
本研究所采用的白木香种子来源于广东省化州市维国沉香种植开发专业合作社，广州中医药大学中药资源科学与工程研究中心的詹若挺教授通过参考《中国植物志》[16]《中华人民共和国药典》[17]鉴定其为白木香[Aquilariasinensis（Lour.）Gilg]种子。
1.1.2　主要试剂
MS培养基（Murashige & Skoog Medium）购自Duchefa公司；蔗糖、琼脂购自BioFroxx公司；IBA（Indole-3-Butytric acid）购自Sigma公司；NaCl购自天津市大茂化学试剂厂；EASYspin Plus植物快速提取试剂盒购自北京艾德莱生物科技有限公司。
1.2　方法
1.2.1　材料的获取
白木香的离体根获取过程涉及连续三代继代培养，每次继代均分为2个阶段：培养阶段和盐胁迫阶段。培养阶段：首先通过无菌条件培育白木香组培苗，筛选出长势良好的无菌苗根，剪去根尖，并剪成大约2.0 cm的根段。将根段置于含1.0 mg/L IBA的1/2MS液体培养基，培养7 d后，将根段转移至不含IBA的1/2MS培养基中，继续培养42 d（期间每7 d更换1次培养基），从而获得初始的离体根材料。接下来，进行第一次继代。盐胁迫阶段：将离体根材料置于含150 mmol/L NaCl的1/2MS液体培养基中，在（25±1）℃的温度下，以110 r/min的速度震荡培养3 d，之后从数瓶中取出离体根，剪下侧根并将其标记为第一代（G1），立即放入液氮速冻，并储存在–80 ℃的冰箱中。剩余的离体根则继续剪下侧根，置于新的培养基中进行下一代的培养阶段，即在不含NaCl的1/2MS中继续培养，为后续盐胁迫做准备。同样的过程重复进行2次，分别获得第二代（G2）和第三代（G3）的盐胁迫侧根材料。每次继代都遵循先培养后胁迫模式，确保每代侧根都经历相同的处理流程。最后，将G1、G2、G3用于Small RNA测序。
1.2.2　Small RNA文库构建与HiSeq2500测序
采用EASYspin Plus植物快速提取试剂盒提取经过胁迫处理的白木香离体根样品的总RNA。随后，将提取的高质量RNA样本送至广州基迪奥生物科技有限公司，构建文库。文库构建完成后，采用Illumina HiSeq 2500测序平台进行测序。
1.2.3　基因表达量分析
对测序得到的raw data文件进行数据过滤，剔除低质量的reads、不带有3ʹ接头的reads及含有5'接头的reads，最后得到Small RNA的tag序列。接着，利用GenBank和Rfam（11.0）数据库来对这些tag序列进行注释，尽可能地识别并剔除样本中可能存在的rRNA，scRNA、snoRNA、snRNA和tRNA。将最终得到的tag序列同miRBase中已知的植物或动物miRNA进行比对，鉴定到的miRNA即为已知miRNA。去除鉴定为已知的miRNA，挑选出能够比对上基因组的tag，使用软件MIREAP v0.2预测miRNA特殊的二级结构，找出可能存在的新的miRNA。对各个样品鉴定的miRNA进行汇总，并依据TPM（tags per million）公式计算每个miRNA的表达量，TPM=T×106/N[T表示miRNA的tags，N表示总miRNA的tags（已存在+已存在编辑+已知+新预测miRNA counts数之和）]。通过这一过程，获得所有样品的全部miRNA的表达谱。
1.2.4　miRNA的靶基因预测及靶基因富集分析
使用patmatch v1.2软件对样本中的miRNA和靶基因进行互补配对分析，并设定严格的筛选标准预测最终结果。筛选标准包括：整个互补关系中最多允许4个错配（其中G-U配对视为0.5个错配），且不允许连续错配；miRNA的5'端第2~12位及miRNA与靶基因的第10~11位必须完全匹配，不允许错配；miRNA与靶基因的5'端1~12位置内，最多允许2.5个错配；同时，miRNA与靶基因的最小自由能（MFE）需达到或超过完美匹配时MFE的60%。完成预测后，将所得的靶基因与GO、KEGG数据库进行比对，以进行功能上的注释及分类处理，从而获取有关这些靶基因的详细注释信息。
2　结果与分析
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2.1　所有样本中miRNA图谱概述
高通量测序结果显示，白木香离体根盐胁迫样品（G1-1、G1-2、G1-3、G2-1、G2-2、G2-3、G3-1、G3-2和G3-3）miRNA文库中，所有样品的clean tags均大于85%（表1），表明所得miRNA数据可靠，可用于后续分析。miRNA测序得到的tag序列长度主要分布在21 nt和24 nt（图1），与植物中miRNA的分布相符合。基于miRBase和参考基因组对miRNA进行鉴定，在白木香样品G1-1、G1-2、G1-3、G2-1、G2-2、G2-3、G3-1、G3-2、G3-3中分别发现了282、119、107、94、230、120、365、278、261个已知miRNA，421、149、194、106、424、143、435、284、381个新miRNA，共鉴定出1476个miRNA（图2）。G3代样品中已知miRNA和新miRNA的数量明显多于G1和G2代，表明随着盐胁迫代数的增加，白木香离体根的miRNA表达调控更加复杂，可能涉及更多的基因表达调控过程。
2.2　盐胁迫下miRNA的表达量分析
所有样品中共鉴定出1476个miRNA，包括794个已知miRNA和682个新预测miRNA。在已知miRNA中，miR166-y的表达量最高，在G3样本中其表达量达到6 264 167.887，其次是miR396-x和miR156-x；在新预测miRNA中，novel-m0109-3p的表达量最高，在G3样本中其表达量为30 391.845，其次是novel-m0497-3p和novel-m0108-3p（表2）。进一步分析3个样品中miRNA的差异表达，发现miR166-y、miR396-x和novel-m0109-3p在G3中的表达占优势，novel-m0224-3p和novel-m0213-5p在G2中的表达量较高，novel-m0497-3p在G1中表达量较高。
2.3　盐胁迫下miRNA差异表达分析
使用edgeR软件（默认参数）对miRNA进行差异分析（图3A）。差异miRNA是以表达量变化2倍以上，并且P值小于0.05作为筛选标准。在鉴定出的1465个miRNA中有59个miRNA差异表达（21个上调，38个下调）。在G1 vs G2检测出3个差异表达miRNA（1个上调和2个下调）；在G1 vs G3中检测出26个差异表达miRNA（7个上调和19个下调）；在G2 vs G3中检测出30个差异表达miRNA（13个上调和17个下调）。为了更清晰地揭示3组中差异基因的表达趋势，筛选并整理每组中排名前10的上调/下调miRNA（表3）。在G1 vs G3中，novel-m0141-5p和novel-m0098-3p是显著上调的差异miRNA，而novel-m0561-3p和miR7757-y则显著下调；G2 vs G3中，novel-m0098-3p和miR7494-y呈显著性上调，而novel-m0628-5p和miR5185-y则显著下调。结合韦恩图分析（图3B），得出G1 vs G2和G1 vs G3两组间共有1个差异miRNA，G1 vs G2和G2 vs G3两组间共有1个差异miRNA，G1 vs G3和G2 vs G3两组间共有10个差异miRNA。在G1 vs G2、G1 vs G3和G2 vs G3三组中分别有1、15、19个差异miRNA特异性表达。3个比较组中没有共同的差异表达miRNA。
2.4　差异靶基因GO功能注释
为了筛选出白木香三代离体根中与盐胁迫应答及次生代谢物产生相关的miRNA，使用PatMatch软件对白木香一代、二代和三代盐胁迫下离体根的全部miRNA基因进行预测，共得到靶基因13 617个，靶基因位点23 504个。其中，已知miRNA预测到的靶基因有13 276个，靶基因位点22 285个；而预测到的新miRNA靶基因有935个，靶基因位点1 219个。差异表达miRNA通过改变其靶基因的表达模式参与植物胁迫应答[18]。因此，对筛选得到的275个差异miRNA靶基因进行GO功能注释，其按照生物学过程、分子功能和细胞组分分为3类（图4），其中生物学过程涉及的GO条目最多，有19个；分子功能和细胞组分涉及的条目分别为8个和9个。在生物学过程中主要富集在细胞过程（cellular process）、代谢过程（metabolic process）和单一有机体过程（single organism process），相关的靶基因数目分别为91、88和64；在分子功能方面主要富集在催化活性（catalytic activity）和结合（binding），相关的靶基因数目分别为81和56；在细胞组成部分主要富集在细胞部分（cell part）、细胞（cell）和细胞器（organelle），相关的靶基因数目分别为44、44和40。
2.5　差异靶基因KEGG富集分析
为了进一步了解差异靶基因的生物学功能，本研究对各组间差异表达的miRNA的靶基因进行富集分析（图5）。结果表明，显著富集的通路有40条，涉及57条差异表达的miRNA靶基因。其中，涉及代谢通路、植物次生代谢和植物激素信号传导途径的靶基因较多，分别是16、11和5个。将参与关键代谢途径中富集的靶基因与对应的miRNA进行联合分析及NR注释（表4），发现富集到的代谢通路共涉及了6个下调和4个上调的差异miRNA。其中下调的miRNA包括miR477-y、miR5185-y、novel-m0161-3p、novel-m0628-5p、miR408-z和miR7757-y，而上调的miRNA包括miR7494-y、novel-m0098-3p、novel-m0320-3p和miR8020-x。这些miRNA在特定的比较组中具有特异性表达：miR477-y、miR408-z、miR7757-y、novel-m0161-3p在G1 vs G3中特异性表达，而miR5185-y、miR7494-y、novel-m0628-5p、novel-m0320-3p和miR8020-x则在G2 vs G3中特异性表达。进一步分析发现，下调的miRNA靶基因主要涉及糖酵解/糖异生成、苯丙烷类生物合成、植物激素信号传导、植物病原相互作用等信号通路。而上调的miRNA靶基因则主要参与类黄酮生物合成、谷胱甘肽代谢等信号通路。
NR注释结果显示，miR8020-x的靶基因与查尔酮黄酮异构酶有关；miR7494-y的2个靶基因分别可能与谷胱甘肽过氧化物酶和丝氨酸/苏氨酸蛋白激酶有关；miR5185-y的靶基因与含F-box/WD重复蛋白相关；miR477-y的靶基因与lysM结构域受体样激酶3相关；miR7757-y的靶基因与生长因子B3家族蛋白/辅助因子AUX/IAA相关同工酶1相关；miR408-z与类生长素反应蛋白IAA6相关；novel-m0628-5p与有丝分裂原活化蛋白激酶2同工酶X1有关。
3　讨论
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3.1　可能参与白木香离体根次生代谢产物有关的miRNA
结合GO功能注释、KEGG富集分析及差异miRNA的NR注释，发现靶基因主要在细胞过程、代谢过程和催化活化等功能和植物激素信号传导代谢途径富集。部分miRNA靶基因可能与白木香次生代谢产物有关，而另一些miRNA靶基因则可能与白木香离体根响应盐胁迫相关。在三代盐胁迫处理的离体根中共获得59个差异miRNA，其中，在G1 vs G2、G1 vs G3、G2 vs G3三个比较组中分别有1、7、13个上调的差异miRNA，有2、19、17个下调的差异miRNA。上调差异miRNA随着胁迫代数的增加逐渐增加，在G1 vs G3和G2 vs G3两个比较组过渡中下调差异miRNA反而减少了，这暗示了白木香在连续多代盐胁迫下，其基因表达调控发生了复杂的变化。
查尔酮异构酶基因（CHI）的表达可以促进植物体内黄酮类次生代谢物的合成[19]。本研究中miR8020-x预测的靶基因evm.model.Scaffold446.31与查尔酮异构酶相关。因此，推测miR8020-x可能通过影响靶基因表达水平来调节次生代谢途径中查尔酮异构酶的活性，从而影响类黄酮次生代谢物的合成，但这还需要进一步的实验验证。此外，差异基因novel-m0628-5p的靶基因evm. model.Scaffold139.25和evm.model.Scaffold43.133分别与CBSX3和有丝分裂原活化蛋白激酶（MAPK）相关，而CBSXs参与拟南芥的组织发育和胁迫响应过程[20]，MAPKK可能参与沉香中2-苯乙基色酮的生物合成[21]。因此，本研究推测差异基因novel-m0628-5p不仅响应白木香离体根盐胁迫，还可能参与白木香中2-（2-苯乙基）色酮类物质的合成。
3.2　可能参与白木香离体根抵御盐胁迫有关的miRNA
在盐胁迫环境下，胡杨（Populus euphratica）能够上调谷胱甘肽过氧化物酶的表达，维持总体抗氧化活性[22]。本研究发现，特定miRNA如miR7494-y的靶基因evm.model.Scaffold195.28与谷胱甘肽过氧化物酶2相关，并参与过氧化物酶活性（GO:0004601）、毒素代谢过程（GO:0009404）、激素介导的信号通路（GO:0009755）等过程；其靶基因evm.model.scaffold7.53调节丝氨酸/苏氨酸蛋白激酶活性，参与植物信号传导通路。因此，推测miR7494-y通过调控靶基因evm.model. Scaffold195.28和靶基因evm.model.scaffold7.53的表达，增强白木香离体根在盐胁迫下的抗氧化能力和信号传导，从而提高其耐盐性。本研究中，差异miR5185-y预测的靶基因evm.model. Scaffold140.3与F-box相关，而F-box蛋白家族成员也广泛参与植物逆境响应[23]。因此，本研究推测miR5185-y参与离体根响应盐胁迫。
miR477在茶树（Camellia sinensis）中对逆境（如干旱、盐等）的响应起着重要的调控作用[24]。miR7757参与小麦（Triticum aestivum）种子萌发过程[25]。在拟南芥中的研究表明，miR408的过表达能增强其对盐度、寒冷及氧化应激耐受，但提高了对干旱和渗透胁迫敏感性[26]。在本研究中，miR477-y，miR7757-y和miR408-z呈现出差异表达，说明这些miRNA可能与白木香响应盐胁迫有着重要的相关作用。已知LysM类受体激酶在植物抗逆及防御机制中起关键作用，并且，在战明慧[27]的研究中，发现苹果（Malus pumila）中的LysM类受体激酶MdLYK15负调控苹果对腐皮镰孢菌的抗性。而本研究发现，miR477-y的靶基因evm.model.Scaffold8.140与含有lysM结构域的受体样激酶相关，该基因参与植物病原体相互作用，并可能通过调控离体根来增强对盐胁迫的抵御能力。此外，CBSXs蛋白和AUX/IAA蛋白等也被证实参与植物的胁迫响应过程[20,28]。本研究发现，差异表达基因miR7757-y的靶基因evm. model.Scaffold24.124调控植物激素信号传导中的AUX/IAA蛋白，而miR408-z的靶基因evm.model. Scaffold403.11则调控生长素反应蛋白IAA6，这些调控作用共同影响了白木香离体根的生长和对盐胁迫的适应能力。综上所述，本研究推测miR 8020-x和novel-m0628-5p可能参与白木香离体根次生代谢产物的合成，而miR7494-y、miR477-y、miR5185-y、miR7757-y、miR408-z和novel-m0628-5p则可能参与白木香离体根对盐胁迫的响应。然而，本研究尚未对这些miRNA进行功能验证及开展深入的作用机制研究。特别是在分析过程中，尚未获得直接证据来证实分析中的差异miRNA与“记忆”相关。因此，后续将聚焦于对这些差异miRNA的功能验证，旨在明确它们在盐胁迫过程中的具体作用机制，并进一步探索它们与胁迫“记忆”特征之间的潜在联系。
基金
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  • 广东省乡村振兴战略专项-农业科技发展及资源环境保护管理项目-广东省现代南药产业技术体系创新团队项目(2023KJ148)
文献
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2025年第46卷第4期
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doi: 10.3969/j.issn.1000-2561.2025.04.005
  • 接收时间：2024-11-26
  • 首发时间：2026-06-24
  • 出版时间：2025-04-25
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  • 收稿日期：2024-11-26
  • 录用日期：2024-12-03
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广东省乡村振兴战略专项-农业科技发展及资源环境保护管理项目-广东省现代南药产业技术体系创新团队项目(2023KJ148)
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    广州中医药大学中药学院/岭南中药资源教育部重点实验室/国家中成药工程技术研究中心南药研发实验室，广东广州　510006

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* 马新业（MA Xinye），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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