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Article(id=1198656218324628363, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1198656209390764948, articleNumber=null, orderNo=null, doi=10.16438/j.0513-4870.2023-0426, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1681056000000, receivedDateStr=2023-04-10, revisedDate=1690387200000, revisedDateStr=2023-07-27, acceptedDate=null, acceptedDateStr=null, onlineDate=1763711512403, onlineDateStr=2025-11-21, pubDate=1697040000000, pubDateStr=2023-10-12, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1763711512403, onlineIssueDateStr=2025-11-21, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1763711512403, creator=13701087609, updateTime=1763711512403, updator=13701087609, issue=Issue{id=1198656209390764948, tenantId=1146029695717560320, journalId=1189982191388893191, year='2023', volume='58', issue='10', pageStart='2835', pageEnd='3150', issueExtLink='null', onlineDate='null', pubDate='1697040000000', pubDateStr='2023-10-12', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1763711510274, creator='13701087609', updateTime=1763711659007, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1198656833280897539, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1198656209390764948, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1198656833280897540, tenantId=1146029695717560320, journalId=1189982191388893191, issueId=1198656209390764948, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=3130, endPage=3139, ext={EN=ArticleExt(id=1198656218714698651, articleId=1198656218324628363, tenantId=1146029695717560320, journalId=1189982191388893191, language=EN, title=Transcriptome analysis and differential gene screening of Panax ginseng seed in different sand storage stages, columnId=null, journalTitle=Acta Pharmaceutica Sinica, columnName=null, runingTitle=null, highlight=null, articleAbstract=

Analyze the changes in gene expression profiles during the process of Panax ginseng seed dormancy release, and screen for differential genes, providing a basis for analyzing the mechanism of P. ginseng seed dormancy release. Comparative transcriptome analysis was conducted by using RNA-Seq sequencing technology in P. ginseng seeds stored at different low temperature. A total of 80.97 Gb of Raw reads and 80.19 Gb of Clean reads were obtained from the transcriptome. Principal component analysis and correlation analysis showed that there were significant differences in gene expression patterns at different developmental stages. Upset results showed that 46 248 unigenes were co-expressed in four stages, and 414, 445, 400 and 389 unigenes were specifically expressed in 0, 8, 14 and 28 days, respectively. Gene Ontology functional annotation showed that the differentially expressed genes were mainly involved in nsaturated fatty acid biosynthetic process, nuclear body and oxidoreductase activity. Encyclopedia of Genes and Genomes metabolic pathway showed that differentially expressed genes were mainly involved in peroxisome, mitogen-activated protein kinase signaling pathway-plant, plant hormone signal transduction, ribosome, biosynthesis of unsaturated fatty acid, circadian rhythm-plant and other metabolic pathways. In the process of P. ginseng seed dormancy release, multiple biological processes, such as unsaturated fatty acid biosynthesis and plant hormone signal transduction, are required to coordinate regulation, which constitutes a complex dormancy release regulation network. Transcriptome analysis and differential gene screening of P. ginseng seeds at different sand storage time laid a foundation for the analysis of P. ginseng seed dormancy release mechanism and molecular breeding.

, authors=null, authorsList=Guang-fei WEI, An-ning LI, Jia XU, Shi-lin CHEN, Lin-lin DONG, authorCompany=null, correspAuthors=Lin-lin DONG, authorNote=null, correspAuthorsNote=null, copyrightStatement=Copyright ©2023 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=1198656221520687192, articleId=1198656218324628363, tenantId=1146029695717560320, journalId=1189982191388893191, language=CN, title=不同沙藏时间人参种子转录组分析及差异基因筛选, columnId=1190335348896011050, journalTitle=药学学报, columnName=研究论文, runingTitle=null, highlight=null, articleAbstract=

分析人参种子休眠解除过程中基因表达谱的变化情况, 并筛选其差异基因, 为解析人参种子休眠解除机制提供依据。以低温沙藏不同时间的人参种子为研究材料, 利用转录组测序技术进行比较分析。转录组共获得80.97 Gb Raw reads和80.19 Gb Clean reads。主成分分析和相关性分析表明基因在不同发育时期具有不同的表达模式且存在显著差异。可视化集合图显示有46 248个unigenes在四个时期共表达, 有414、445、400和389个unigenes分别在低温沙藏0、8、14和28天特异表达。基于基因本体数据库功能注释显示差异表达基因主要参与不饱和脂肪酸生物合成进程、核质体和氧化还原酶活性等。基于京都基因与基因组百科全书数据库代谢途径显示差异表达基因主要参与过氧物酶体、蛋白激酶信号通路-植物、植物激素信号转导、核糖体、不饱和脂肪酸的生物合成、植物生理节律等代谢通路。人参种子休眠解除过程中需要不饱和脂肪酸生物合成和植物激素信号转导等多个生物过程的协同调控, 构成复杂的休眠解除调控网络。不同沙藏时间人参种子转录组分析及差异基因的筛选, 为解析人参种子休眠解除机制、开展人参分子育种奠定基础。

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*董林林, E-mail:
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Physiol Plant, 2018, 167: 597-612, articleTitle=Illumina-based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after-ripening process, refAbstract=null)], funds=[Fund(id=1198960249962066675, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, awardId=ZXKT21037, language=CN, fundingSource=中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT21037), fundOrder=null, country=null), Fund(id=1198960250092090110, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, awardId=ZZ15-YQ-044, language=CN, fundingSource=中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ15-YQ-044), fundOrder=null, country=null), Fund(id=1198960250213724942, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, awardId=ZXKT22001, language=CN, fundingSource=中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT22001), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1198960243305705512, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, xref=null, ext=[AuthorCompanyExt(id=1198960243314094123, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, companyId=1198960243305705512, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1. 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Jilin Aodong Medicinal Seed Technology Co., Ltd., Yanbian 000623, China), AuthorCompanyExt(id=1198960243515420731, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, companyId=1198960243494449208, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.吉林敖东药材种业科技有限公司, 吉林 延边 000623)])], figs=[ArticleFig(id=1198960247546147312, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=0DB8lLDxDstOnAa3qyDt0w==, figureFileBig=GVi4VVuv6c68fos+CGyHRA==, tableContent=null), ArticleFig(id=1198960247667782145, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 1, caption= Changes of seed morphology after TTC staining, embryo diameter, survival rate and conductivity at different developmental stages. A: TTC staining; B: Embryo diameter; C: Survival rate; D: Conductivity. TTC: 2, 3, 5-Triphenyl-2<i>H</i>-tetrazolium chloride. RS0, RS8, RS14 and RS28: 0, 8, 14 and 28 days of low temperature sand storage, respectively. a, b, c and d: Significant differences of different groups , figureFileSmall=0DB8lLDxDstOnAa3qyDt0w==, figureFileBig=GVi4VVuv6c68fos+CGyHRA==, tableContent=null), ArticleFig(id=1198960247881691680, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=VLIJ1O4n4cl371y/MPX55A==, figureFileBig=ecAaui/qz2rYGm3Nixdueg==, tableContent=null), ArticleFig(id=1198960247982354985, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 2, caption= Analysis of gene expression at different developmental stages. A: Principal component analysis; PCA1: Principal component analysis 1; PCA2: Principal component analysis 2; B: Pearson correlation between samples; R: The coefficient of correlation; C: Upset profiles of genes; D: Numbers of differentially expressed genes; Up: Up genes; Down: Down genes , figureFileSmall=VLIJ1O4n4cl371y/MPX55A==, figureFileBig=ecAaui/qz2rYGm3Nixdueg==, tableContent=null), ArticleFig(id=1198960248120767033, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=N8EmBlPVzAx/dChwneXYWQ==, figureFileBig=xjG0aNM1fC8PohHrPMfr8w==, tableContent=null), ArticleFig(id=1198960248254984772, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 3, caption= Heat maps of differentially expressed genes at different developmental stages , figureFileSmall=N8EmBlPVzAx/dChwneXYWQ==, figureFileBig=xjG0aNM1fC8PohHrPMfr8w==, tableContent=null), ArticleFig(id=1198960248443728466, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=2r3V/W3H3pzybukfSGahjg==, figureFileBig=ALgcIPkh9dESndxRV+U/lA==, tableContent=null), ArticleFig(id=1198960248548586078, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 4, caption= Annotated enrichment circles of GO and KEGG genes at different developmental stages. A: GO enrichment circles; GO: Gene ontology; B. KEGG enrichment circles; KEGG: Encyclopedia of genes and genomes. The first circle of enrichment circles (from outside to inside) is the GO/KEGG entries of enrichment Top (minimum <i>P</i> value), and the outer circle is the coordinate scale of gene number. Different colors represent the classification of GO/KEGG three categories. The second circle represents the number of genes annotated to GO/KEGG entries, and the color represents the -log<sub>10</sub> value of enrichment analysis <i>P</i>-value. The third circle is the number of different genes in GO/KEGG. The fourth circle represents the percentage of enrichment factor , figureFileSmall=2r3V/W3H3pzybukfSGahjg==, figureFileBig=ALgcIPkh9dESndxRV+U/lA==, tableContent=null), ArticleFig(id=1198960248686998126, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=Z97RSxdx0T++buhfALByyQ==, figureFileBig=/2AMH54T9rof+bvND5R18g==, tableContent=null), ArticleFig(id=1198960248863158908, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 5, caption= Heat maps of different genes annotated to the GO enrichment pathway at different developmental stages. A: GO0006636 pathway; B: GO0016604 pathway; C: GO0016717 pathway , figureFileSmall=Z97RSxdx0T++buhfALByyQ==, figureFileBig=/2AMH54T9rof+bvND5R18g==, tableContent=null), ArticleFig(id=1198960248972210829, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=qXCTPdICiSgsIKA/dll0GQ==, figureFileBig=9YzapNhGIKneZRKk/bJsjg==, tableContent=null), ArticleFig(id=1198960249110622875, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 6, caption= Differential gene heat maps annotated to KEGG metabolic pathway map04075 at different developmental stages. A: 114 genes; B: 113 genes , figureFileSmall=qXCTPdICiSgsIKA/dll0GQ==, figureFileBig=9YzapNhGIKneZRKk/bJsjg==, tableContent=null), ArticleFig(id=1198960249223869094, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=ttu3ypahFgX3ViRlJCBNXg==, figureFileBig=U0F2SEB6BFEwgfi8BFCKOg==, tableContent=null), ArticleFig(id=1198960249408418489, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Figure 7, caption= Differential gene heat maps annotated to KEGG metabolic pathway map01040 at different developmental stages , figureFileSmall=ttu3ypahFgX3ViRlJCBNXg==, figureFileBig=U0F2SEB6BFEwgfi8BFCKOg==, tableContent=null), ArticleFig(id=1198960249534247619, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=EN, label=null, caption=null, figureFileSmall=null, figureFileBig=null, tableContent=
Sample name Raw reads Raw bases /Gb Clean reads Clean bases /Gb Effective base percentage/% Q20/% Q30/% GC/%
RS0_1 43281910 6.49 42882418 6.43 99.08 100.00 97.94 45
RS0_2 44748280 6.71 44291900 6.64 98.98 100.00 98.03 45
RS0_3 47440696 7.12 46984626 7.05 99.04 100.00 98.23 45
RS8_1 44406184 6.66 43970880 6.60 99.02 100.00 98.07 44
RS8_2 45777636 6.87 45324690 6.80 99.01 100.00 98.02 45
RS8_3 44645836 6.70 44202686 6.63 99.01 100.00 98.22 45
RS14_1 44020644 6.60 43605014 6.54 99.06 100.00 97.95 45
RS14_2 45107560 6.77 44680586 6.70 99.05 100.00 98.10 45
RS14_3 47698750 7.15 47268012 7.09 99.10 100.00 97.82 45
RS28_1 43466424 6.52 43055738 6.46 99.06 100.00 98.15 44.50
RS28_2 43195760 6.48 42802500 6.42 99.09 100.00 98.25 45
RS28_3 45971348 6.90 45504764 6.83 98.99 100.00 97.94 45
), ArticleFig(id=1198960249668465365, tenantId=1146029695717560320, journalId=1189982191388893191, articleId=1198656218324628363, language=CN, label=Table 1, caption=

Statistical table of effective data evaluation

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Sample name Raw reads Raw bases /Gb Clean reads Clean bases /Gb Effective base percentage/% Q20/% Q30/% GC/%
RS0_1 43281910 6.49 42882418 6.43 99.08 100.00 97.94 45
RS0_2 44748280 6.71 44291900 6.64 98.98 100.00 98.03 45
RS0_3 47440696 7.12 46984626 7.05 99.04 100.00 98.23 45
RS8_1 44406184 6.66 43970880 6.60 99.02 100.00 98.07 44
RS8_2 45777636 6.87 45324690 6.80 99.01 100.00 98.02 45
RS8_3 44645836 6.70 44202686 6.63 99.01 100.00 98.22 45
RS14_1 44020644 6.60 43605014 6.54 99.06 100.00 97.95 45
RS14_2 45107560 6.77 44680586 6.70 99.05 100.00 98.10 45
RS14_3 47698750 7.15 47268012 7.09 99.10 100.00 97.82 45
RS28_1 43466424 6.52 43055738 6.46 99.06 100.00 98.15 44.50
RS28_2 43195760 6.48 42802500 6.42 99.09 100.00 98.25 45
RS28_3 45971348 6.90 45504764 6.83 98.99 100.00 97.94 45
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不同沙藏时间人参种子转录组分析及差异基因筛选
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尉广飞 1 , 李安宁 2 , 徐佳 1 , 陈士林 1 , 董林林 1, *
药学学报 | 研究论文 2023,58(10): 3130-3139
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药学学报 |研究论文 2023 , 58 (10) : 3130 -3139
不同沙藏时间人参种子转录组分析及差异基因筛选
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尉广飞1, 李安宁2, 徐佳1, 陈士林1, 董林林1, *
作者信息
  • 1.中国中医科学院中药研究所, 北京 100700
  • 2.吉林敖东药材种业科技有限公司, 吉林 延边 000623
通讯作者:
*董林林, E-mail:
Transcriptome analysis and differential gene screening of Panax ginseng seed in different sand storage stages
Guang-fei WEI1, An-ning LI2, Jia XU1, Shi-lin CHEN1, Lin-lin DONG1, *
Affiliations
  • 1. Institute of Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
  • 2. Jilin Aodong Medicinal Seed Technology Co., Ltd., Yanbian 000623, China
出版时间: 2023-10-12 doi: 10.16438/j.0513-4870.2023-0426
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摘要
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分析人参种子休眠解除过程中基因表达谱的变化情况, 并筛选其差异基因, 为解析人参种子休眠解除机制提供依据。以低温沙藏不同时间的人参种子为研究材料, 利用转录组测序技术进行比较分析。转录组共获得80.97 Gb Raw reads和80.19 Gb Clean reads。主成分分析和相关性分析表明基因在不同发育时期具有不同的表达模式且存在显著差异。可视化集合图显示有46 248个unigenes在四个时期共表达, 有414、445、400和389个unigenes分别在低温沙藏0、8、14和28天特异表达。基于基因本体数据库功能注释显示差异表达基因主要参与不饱和脂肪酸生物合成进程、核质体和氧化还原酶活性等。基于京都基因与基因组百科全书数据库代谢途径显示差异表达基因主要参与过氧物酶体、蛋白激酶信号通路-植物、植物激素信号转导、核糖体、不饱和脂肪酸的生物合成、植物生理节律等代谢通路。人参种子休眠解除过程中需要不饱和脂肪酸生物合成和植物激素信号转导等多个生物过程的协同调控, 构成复杂的休眠解除调控网络。不同沙藏时间人参种子转录组分析及差异基因的筛选, 为解析人参种子休眠解除机制、开展人参分子育种奠定基础。

人参种子  /  休眠解除  /  转录组  /  差异基因  /  功能注释

Analyze the changes in gene expression profiles during the process of Panax ginseng seed dormancy release, and screen for differential genes, providing a basis for analyzing the mechanism of P. ginseng seed dormancy release. Comparative transcriptome analysis was conducted by using RNA-Seq sequencing technology in P. ginseng seeds stored at different low temperature. A total of 80.97 Gb of Raw reads and 80.19 Gb of Clean reads were obtained from the transcriptome. Principal component analysis and correlation analysis showed that there were significant differences in gene expression patterns at different developmental stages. Upset results showed that 46 248 unigenes were co-expressed in four stages, and 414, 445, 400 and 389 unigenes were specifically expressed in 0, 8, 14 and 28 days, respectively. Gene Ontology functional annotation showed that the differentially expressed genes were mainly involved in nsaturated fatty acid biosynthetic process, nuclear body and oxidoreductase activity. Encyclopedia of Genes and Genomes metabolic pathway showed that differentially expressed genes were mainly involved in peroxisome, mitogen-activated protein kinase signaling pathway-plant, plant hormone signal transduction, ribosome, biosynthesis of unsaturated fatty acid, circadian rhythm-plant and other metabolic pathways. In the process of P. ginseng seed dormancy release, multiple biological processes, such as unsaturated fatty acid biosynthesis and plant hormone signal transduction, are required to coordinate regulation, which constitutes a complex dormancy release regulation network. Transcriptome analysis and differential gene screening of P. ginseng seeds at different sand storage time laid a foundation for the analysis of P. ginseng seed dormancy release mechanism and molecular breeding.

Panax ginseng seed  /  dormancy release  /  transcriptome  /  differentially expressed gene  /  functional annotation
尉广飞, 李安宁, 徐佳, 陈士林, 董林林. 不同沙藏时间人参种子转录组分析及差异基因筛选. 药学学报, 2023 , 58 (10) : 3130 -3139 . DOI: 10.16438/j.0513-4870.2023-0426
Guang-fei WEI, An-ning LI, Jia XU, Shi-lin CHEN, Lin-lin DONG. Transcriptome analysis and differential gene screening of Panax ginseng seed in different sand storage stages[J]. Acta Pharmaceutica Sinica, 2023 , 58 (10) : 3130 -3139 . DOI: 10.16438/j.0513-4870.2023-0426
正文
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人参为五加科(Araliaceae) 人参属(Panax) 植物人参Panax ginseng C. A. Mey.的干燥根及根茎, 被称为“草药之王”[1]。人参含有人参皂苷、多糖和氨基酸等化学成分[2]。现代药理学研究[3]表明人参具有抗肿瘤、抗哮喘、抗抑郁、抗疲劳、抗病毒、抗氧化、抗溃疡等多种作用。由于过度采挖和适生环境的破坏, 人参野生资源日渐枯竭, 目前人参主要依靠人工栽培。人参主要以种子进行繁殖, 然而人参种子具有休眠特性, 休眠期较长, 在常温下不能萌发[4]。为确保人参产业的可持续发展, 需要迫切解析人参种子休眠解除的分子机制。
人参种子采收后必须经过沙藏处理或者应用植物生长调节剂进行化学处理, 才能完成种子胚形态后熟和生理后熟两个阶段, 解除休眠而发芽生长[5]。人参种子休眠受多种因素的影响和多种物质的控制。研究表明, 人参种子需要在15 ℃条件下湿沙储藏90天, 种子胚才能发育完成, 开始萌发; 而人参种子的生理后熟需要在5 ℃条件下继续沙藏90天, 才能解除休眠, 出苗生长[6]。赤霉酸(gibberellin A3, GA3) 和6-苄基腺嘌呤(6-benzylaminopurine, 6-BA) 等植物生长调节剂混合水溶液可显著提高人参种子裂口率、胚率和出苗率[7]。施加外源GA3可以明显促进人参种子生理休眠的打破, 发芽率较对照组提升52.53%[8]。目前, 关于人参种子休眠或萌发的报道大多集中在温度和植物激素处理及其生理指标的检测等方面。关于人参种子休眠解除机制的报道很少, 特别是与人参种子休眠解除过程相关的基因和调控网络尚不清晰。
种子休眠是植物复杂的自我保护机制, 需要经过漫长的生物进化过程才能形成完善的基因控制过程。有学者利用转录组学在白鲜[9]、华重楼[10]和天麻[11]种子休眠解除机制的研究上获得了阶段性成果。本研究以不同低温沙藏时间的人参种子为研究材料, 利用转录组测序技术进行比较分析, 筛选低温沙藏不同时间后种子的差异表达基因, 为揭示人参种子低温沙藏可能解除休眠的分子机制提供了思路和参考, 进而保障人参产业的可持续发展。
材料与方法
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材料  人参种子收集于中国中医科学院中药研究所靖宇县人参基地(E126.8°, N42.39°)。将人参种子去除杂质后, 用1% NaClO浸泡消毒20 min。将经过消毒的湿沙与种子以3∶1体积混匀, 放入4 ℃冰箱中低温沙藏。对照组未经低温沙藏处理(RS0)、低温沙藏8天(RS8)、低温沙藏14天(RS14)、低温沙藏28天(RS28) 共4个发育阶段的人参种子, 一部分用于检测种子存活率和电导率等指标, 一部分用于染色观察种子胚发育的形态变化, 另一部分用于转录组测序分析种子萌发过程的差异基因的变化。
TTC染色、胚直径、存活率和电导率等指标测定  将种子置于三角瓶中, 每份加入等量双蒸水至完全浸没种子, 在25 ℃恒温箱内浸泡12 h[12]。每个处理种子50粒, 重复3次。浸泡后的种子, 用滤纸去除表面的水分, 用解剖刀将种子沿种脐纵切, 置于染色盘内备用。加入浓度为0.3%的2, 3, 5-氯化三苯基四氮唑(2, 3, 5-triphenyl-2H-tetrazolium chloride, TTC) 溶液, 至种子完全浸没。25℃恒温箱内染色12 h之后, 倒出TTC溶液, 用双蒸水冲洗种子3次, 再用滤纸吸干种子表面的水分。观察胚和胚乳的染色效果, 并记录染色情况。
每组取50粒种子, 3个重复, 用游标卡尺测量种子胚直径。
检查种子存活情况, 每隔5天统计1次存活情况[13]。每组设置50个种子, 共设置3次重复。存活率计算: 存活率= (正常存货种子数/供试种子数)×100%。
每组取50粒种子, 3个重复, 准确称重(W)[14]。蒸馏水冲洗3次, 用定性滤纸将表面水分吸干, 分别装入锥形瓶中, 贴上标签, 加入250 mL蒸馏水, 测定初始电导率(d1)。20 ℃条件下, 种子浸泡24 h后再次测定电导率(d2), 每4 h测1次电导率。电导率计算: 电导率= (d2-d1)/W。
RNA提取、文库构建及上机测序  按照多糖多酚植物总RNA提取试剂盒(BioTeke, 北京, 中国) 的操作流程提取人参种子总RNA。RNA纯度(OD260/280, OD260/230) 运用Nanodrop 2000 (Thermo Fisher公司, 美国) 检测, RNA片段长度采用Agilent 2100 (Agilent公司, 美国) 检测。RNA检测合格后用于cDNA文库构建。质量合格的文库利用Illumina HiSeqTM 2000平台进行测序, 测序策略为PE150。所有的测序数据均已上传到NCBI官网, 上传登录号为SAMN33422917-SAMN33422928。
原始数据过滤和转录本拼接  首先利用Fastp (v0.19.3) 软件对原始数据进行过滤获得Clean reads[15]。然后使用Trinity (v2.4.0) 对获得的Clean reads进行转录本组装, 最后使用Corset对组装得到的转录本进行聚类去冗余, 得到unigenes[16]。
差异基因的筛选、GO分析和KEGG分析  对获得的转录组数据进行主成分分析(principal component analysis, PCA) 和相关性分析。利用DEseq软件(1.10.1) 对差异基因(differentially expressed genes, DEGs) 进行筛选[17], 筛选标准为FDR (false discovery rate) < 0.05且log2 |fold change, FC| ≥ 1。基于基因本体(gene ontology, GO) 数据库, 利用GOseq软件(v1.22.0) 对差异基因进行GO富集分析, 并以FDR < 0.05筛选为显著富集通路[18]。基于京都基因与基因组百科全书(Encyclopedia of Genes and Genomes, KEGG) 数据库, 采用KOBAS软件(v3.0) 对显著差异表达基因进行代谢通路富集(FDR < 0.05)[19]。
结果与分析
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1 不同沙藏时间人参种胚染色、胚直径、存活率和电导率变化
在TTC染色下, 低温沙藏0天时人参种子较小, 随着沙藏时间的增长, 种子形态逐渐变大, 在低温沙藏28天时达到最饱和的状态, 胚根开始突破胚乳, 种子逐渐发芽(图 1A)。胚直径在低温沙藏0天时最小, 为0.11 mm, 随着低温沙藏时间的推移不断增加, 在低温沙藏28天时最大, 为0.22 mm (图 1B)。种子存活率随着沙藏时间不断增加, 在低温沙藏28天时存活率(70.37%) 最大(图 1C)。电导率在低温沙藏0天时最大, 达5.13 µS·cm-1·g-1, 随着低温沙藏时间的推移不断降低, 在低温沙藏28天时最低(1.37 µS·cm-1·g-1) (图 1D)。说明随着低温沙藏时间的延长, 种子活力在不断增强。
2 不同沙藏时间人参种子转录组数据质量评价
通过转录组测序共获得80.97 Gb Raw reads, 过滤后共获得80.19 Gb Clean reads, 各样本的Q30%碱基比均在97.00%以上, 有效碱基比达到98.00%以上, GC%含量达到44.50%以上(表 1)。由此可见人参种子转录组数据质量较高, 从而为后续信息学注释及差异基因的筛选奠定了基础。
3 不同沙藏时间人参种子转录组基因表达谱分析
对获得的转录组数据进行主成分分析和相关性分析, 结果表明不同时期的人参种子存在显著差异(图 2)。主成分分析显示不同时期的人参种子各自聚为一类(图 2A)。基因表达量相关性图显示不同时期的种子基因表达量存在较低的相关性(图 2B)。Upset结果显示有46 248个unigenes在四个时期样本中共表达, 有414、445、400和389个unigenes分别在低温沙藏0、8、14和28天的人参种子中特异表达(图 2C)。
在休眠解除过程中, 低温沙藏8天的种子与未经低温沙藏处理的种子相比, 上调表达的差异基因为159个, 下调表达的差异基因为60个, 上调基因数大于下调基因数(图 2D)。低温沙藏14天的种子与未经低温沙藏处理的种子相比, 上调表达的差异基因为246个, 下调表达的差异基因为167个, 上调基因数大于下调基因数。低温沙藏28天的种子与未经低温沙藏处理的种子相比, 上调表达的差异基因为203个, 下调表达的差异基因为261个, 上调基因数小于下调基因数。低温沙藏14天的种子与低温沙藏8天的种子相比, 上调表达的差异基因为93个, 下调表达的差异基因为152个, 上调基因数小于下调基因数。低温沙藏28天的种子与低温沙藏8天的种子相比, 上调表达的差异基因为47个, 下调表达的差异基因为115个, 上调基因数小于下调基因数。低温沙藏28天的种子与低温沙藏14天的种子相比, 上调表达的差异基因为36个, 下调表达的差异基因为42个, 上调基因数小于下调基因数。
基于(|log2FC| ≥ 1 & FDR < 0.05) 阈值标准筛选了相对丰度较高的前100个差异表达基因, 在不同沙藏时期具有不同的表达模式(图 3)。其中基因Pg_ S1012.9 (cytochrome P450 CYP71D317)、Pg_S6623.1 (cytochrome P450)、Pg_S3790.7 (probable carboxylesterase 2)、Pg_S3053.13 (protein argonaute 2-like)、Pg_ S6802.1 (heavy metal-associated isoprenylated plant protein, partial) 和Pg_S1073.11 (cytochrome P450 CYP736A12) 在未经低温沙藏处理的种子中显著高表达。基因Pg_S3504.6 (3-ketoacyl-CoA synthase 11-like)、Pg_S1450.35 (ethylene-responsive transcription factor ERF003)、Pg_S4097.1 (delta(12)-fatty-acid desaturase FAD2-like) 和Pg_S1286.2 (probable protein phosphatase 2C 25) 在低温沙藏8天的种子中显著高表达。基因Pg_S6721.2 (calcium-binding allergen Ole e 8)、Pg_ S8293.1 (2-alkenal reductase (NADP(+)-dependent))、Pg_S5335.1 (AP2/ERF transcription factor)、Pg_S4430.5 (protein SRC2-like)、Pg_S1034.30 (dehydration-responsive element-binding protein like) 和Pg_S4624.4 (ethylene-responsive transcription factor ERF053-like) 低温沙藏14天的种子中显著高表达。Pg_S4667.9 (chlorophyll a-b binding protein 8, chloroplastic-like)、Pg_S1518.47 (chlorophyll a/b-binding protein 4)、Pg_S1305.38 (UPF0301 protein SCO2948)、Pg_S3338.3 (ncharacterized protein LOC108205959)、Pg_S6236.9 (uncharacterized protein C24B11.05)、Pg_S3830.15 (UPF0301 protein SCO2948) 和Pg_S4880.12 (protein QUIRKY) 在低温沙藏28天的种子中显著高表达。
4 不同沙藏时间人参种子的差异基因注释分析
为了进一步了解unigene在人参种子休眠解除过程中可能发挥的生物功能, 对获得的差异基因进行Go注释分析(图 4A)。结果表明注释到的unigene可分为生物学进程(biological process)、细胞组成(cellular component) 和分子功能(molecular function)。在生物学进程中Top 3 (P值最小) 为不饱和脂肪酸生物合成进程(GO: 0006636, unsaturated fatty acid biosynthetic process, 71DEGs)、核糖体组装(GO: 0006334, nucleosome assembly, 50DEGs)、几丁质响应(GO: 0010200, response to chitin, 131DEGs)。在细胞组成中Top 3 (P值最小) 为核质体(GO: 0016604, nuclear body, 17DEGs)、核小体(GO: 0000786, nucleosome, 34DEGs)、染色质(GO: 0000790, chromatin, 29DEGs)。在分子功能中Top 3 (P值最小) 为氧化还原酶活性(GO: 0016717, oxidoreductase activity, 61DEGs)、核小体DNA结合(GO: 0031492, nucleosomal DNA binding, 14DEGs)、大核糖体亚基rRNA结合(GO: 0070180, large ribosomal subunit rRNA binding, 18DEGs)。
通过对注释到的unigene进行KEGG代谢通路分析表明, 代谢通路可归为6大类, 如生物学过程(cellular processes)、环境信息处理(environmental information processing)、遗传信息处理(genetic information processing)、人类疾病(human disease)、代谢机制(metabolism) 和组织系统(organismal systems) (图 4B)。在生物学过程中Top 3 (P值最小) 为过氧物酶体(map04146, peroxisome, 64DEGs)、吞噬体(map04145, phagosome, 56DEGs) 和内吞作用(map04144, endocytosis, 101DEGs)。在环境信息处理中Top 3 (P值最小) 为MAPK信号通路-植物(map04016, MAPK signaling pathway-plant, 146DEGs)、植物激素信号转导(map04075, plant hormone signal transduction, 227DEGs) 和ABC转运体(map02010, ABC transporters, 51DEGs)。在遗传信息处理中Top 3 (P值最小) 为核糖体(map03010, ribosome, 234DEGs)、真核生物核糖体的生物发生(map03008, ribosome biogenesis in eukaryotes, 62DEGs) 和内质网蛋白质加工(map04141, protein processing in endoplasmic reticulum, 137DEGs)。在人类疾病中Top 1 (P值最小) 为AGE-RAGE信号通路在糖尿病并发症中的作用(map04933, AGE-RAGE signaling pathway in diabetic complications, 18DEGs)。在代谢机制中Top 3 (P值最小) 为不饱和脂肪酸的生物合成(map01040, biosynthesis of unsaturated fatty acids, 81DEGs)、丙氨酸、天门冬氨酸和谷氨酸代谢(map00250, alanine, aspartate and glutamate metabolism, 39DEGs) 和谷胱甘肽代谢(map00480, glutathione metabolism, 58DEGs)。在组织系统中Top 2 (P值最小) 为植物生理节律(map04712, circadian rhythm-plant, 50DEGs) 和植物-病原菌互作(map04626, plant-pathogen interaction, 124DEGs)。
5 不同沙藏时间人参种子差异基因表达分析
注释到GO富集通路的差异基因在不同发育时期具有不同的表达模式(图 5)。注释到不饱和脂肪酸生物合成进程(GO: 0006636, unsaturated fatty acid biosynthetic process) 的71个DEGs在低温沙藏0天的种子具有较高的表达模式, 随着低温沙藏时间的延长, 表达量逐渐降低, 在低温沙藏28天的种子表达量最低(图 5A)。注释到核质体(GO: 0016604, nuclear body) 的17个DEGs在低温沙藏0天的种子具有较低的表达模式, 随着低温沙藏时间的延长, 表达量逐渐升高, 在低温沙藏28天的种子表达量最高(图 5B)。注释到氧化还原酶活性(GO: 0016717, oxidoreductase activity, 61DEGs) 的61个差异基因在低温沙藏0天的种子具有较高的表达模式, 随着低温沙藏时间的延长, 表达量逐渐降低, 在低温沙藏28天的种子表达量最低(图 5C)。
注释到KEGG富集通路的差异基因在不同发育时期具有不同的表达模式(图 6和7)。注释到植物激素信号转导(map04075, plant hormone signal transduction) 的227个DEGs主要参与了吲哚乙酸(indole-3-acetic acid, IAA)、赤霉素(gibberellin, GA) 和脱落酸(abscisic acid, ABA) 的信号转导过程, 在不同发育时期表现出不同差异(图 6)。注释到不饱和脂肪酸的生物合成(map01040, biosynthesis of unsaturated fatty acids) 的81个DEGs在低温沙藏0天的种子具有较高的表达模式, 随着低温沙藏时间的延长, 表达量逐渐降低, 在低温沙藏28天的种子最低(图 7)。
讨论
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种子活力作为种子质量的重要指标, 不仅影响田间出苗情况, 还影响植株的生长、产量和品质。电导率和TTC染色法是快速、准确测定种子生活力的有效方法[13]。本研究对不同低温沙藏时间的种子存活率、电导率、胚直径和TTC染色法等指标测定, 发现种子存活率、胚直径等都在增加, 说明随着低温沙藏时间的延长, 种子活力在不断增强。
种子休眠是对不利环境的正常反应, 但休眠期过长会影响种子活力和萌发。研究种子萌发前后的生理差异, 首先要了解种子休眠的分子机制。采用转录组技术可以获得大量转录本信息, 已成为研究植物基因和功能的重要手段[20]。本研究对4个不同低温沙藏时间的12份人参种子进行转录组测序分析, 共获得80.19 Gb Clean reads, 数据质量较高, 满足后续信息学注释及差异基因的筛选, 为后续全面了解人参种子休眠机制奠定基础。
Yan等[21]对不同时期的槟榔果皮和种子进行了转录组测序, 发现了大量的参与苯丙烷、莨菪烷类、哌啶和哌啶生物碱和异喹啉生物碱生物合成途径的差异表达基因, 为槟榔基因功能鉴定、次生代谢途径解析及调控机制的研究提供理论依据。对不同发育时期的人参种子进行主成分分析和相关性分析发现不同时期人参种子的表达基因各自聚为一类, 并且不同发育时期的人参种子的基因表达存在差异。这有助于进一步挖掘调控人参种子休眠的差异表达基因, 为人参种子休眠机制的解析提供了基础。
解除种子休眠是一个细胞分裂生长、能量消耗及次生代谢产物重新积累的过程。GO富集分析结果显示与细胞组成相关的差异表达基因在人参种子休眠解除的过程中有大量细胞进行分裂和生长, 进而使得种胚完成形态发育, 表明以上基因积极参与了人参种子的萌发[22]。种子在休眠解除过程中的各种生理反应需要足够的能量, 这些能量主要来源于种子碳水化合物的代谢, 在代谢过程中需要合成大量的酶来催化各种生理生化反应[10]。在分子功能中61个差异表达基因注释为氧化还原酶活性, 说明此过程合成大量的活性酶促进各种生理生化反应, 产生积累足够能源物质[9]。
KEGG功能分析发现差异基因排名靠前的代谢通路分别为不饱和脂肪酸的生物合成、丙氨酸、天门冬氨酸和谷氨酸代谢和谷胱甘肽代谢等途径, 表明人参种子在休眠解除过程中, 需要足够的能量来满足各种生理需求。另外, MAPK信号通路-植物和植物激素信号转导等通路也非常活跃, 且大量DEGs主要富集到了IAA、GA和ABA的信号转导过程, 这一结果与前人[4]研究结果一致。前人[23, 24]研究表明IAA主要调控种胚早期生长、发育和组织分化等, GA主要促进种子萌发生长, ABA主要调控种子休眠。在人参属植物西洋参种子休眠解除和三七种子后熟研究中也发现了大量的差异表达基因参与了植物激素信号转导调控[25, 26]。因此, 植物激素如IAA、GA和ABA等植物激素信号转导过程在人参种子休眠解除过程中发挥重要的作用。
种子的休眠解除和萌发过程是一个非常复杂的过程, 涉及多个代谢途径(包括细胞膜修复、细胞形态构建、次生代谢产物合成、能源产生转换、酶的催化以及植物激素信号转导等) 的相互作用, 构成复杂的休眠解除调控网络。本实验对低温沙藏不同时间的人参种子进行转录组学研究, 获得部分候选差异基因, 但以上结论只是可能与人参种子休眠解除有关, 尚未完全解析其休眠与萌发机制, 缺乏进一步证据证明。后续研究中, 仍需要进行多组学的联合分析与验证, 为解析人参种子休眠解除的分子机制、开展人参分子育种和种质资源开发奠定基础。
作者贡献: 尉广飞负责文章撰写及数据分析; 李安宁负责实验材料的收集; 徐佳负责数据分析和实验材料的收集; 陈士林指导文章撰写并提出修改意见; 董林林负责论文设计及项目开展。
利益冲突: 所有作者均声明不存在利益冲突。
基金
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  • 中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT21037)
  • 中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ15-YQ-044)
  • 中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT22001)
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2023年第58卷第10期
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doi: 10.16438/j.0513-4870.2023-0426
  • 接收时间：2023-04-10
  • 首发时间：2025-11-21
  • 出版时间：2023-10-12
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  • 收稿日期：2023-04-10
  • 修回日期：2023-07-27
基金
中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT21037)
中央级公益性科研院所基本科研业务费专项资金资助项目(ZZ15-YQ-044)
中央级公益性科研院所基本科研业务费专项资金资助项目(ZXKT22001)
作者信息
    1.中国中医科学院中药研究所, 北京 100700
    2.吉林敖东药材种业科技有限公司, 吉林 延边 000623

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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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