Article(id=1277293254131454511, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1277293236137890180, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2024.11.006, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1712764800000, receivedDateStr=2024-04-11, revisedDate=1715529600000, revisedDateStr=2024-05-13, acceptedDate=null, acceptedDateStr=null, onlineDate=1782460042746, onlineDateStr=2026-06-26, pubDate=1732464000000, pubDateStr=2024-11-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782460042746, onlineIssueDateStr=2026-06-26, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782460042746, creator=13701087609, updateTime=1782460042746, updator=13701087609, issue=Issue{id=1277293236137890180, tenantId=1146029695717560320, journalId=1235980609244409860, year='2024', volume='45', issue='11', pageStart='2243', pageEnd='2486', issueExtLink='null', onlineDate='null', pubDate='1732464000000', pubDateStr='2024-11-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782460038455, creator='13701087609', updateTime=1782815269280, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1278783182988358204, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1277293236137890180, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1278783182988358205, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1277293236137890180, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=2287, endPage=2297, ext={EN=ArticleExt(id=1277293256010502705, articleId=1277293254131454511, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Transcriptome Sequencing Analysis of Diseased Pineapple Fruits Stored at Room Temperature after Harvest, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Pineapple is prone to intern browning during storage at room temperature. Diseased and healthy parts of pineapple at early stage of intern browning were used to explore the mechanism of the disease. Three samples from each part were used for transcriptome RNA-Seq analysis. GO, KEGG, cluster analysis of gene expression in various metabolic pathways, and RT-qPCR validation on differential genes were performed and the differential gene expression levels between the diseased (IB) and healthy (WT) parts were compared. IB vs WT had 1037 differentially expressed genes, of which 886 were up-regulated and 130 were down-regulated. GO and KEGG analysis found that the differentially expressed genes in amino acid biosynthesis were the most significant, and the proportion of differentially expressed genes was large. Cluster analysis and RT-qPCR validation found that the sugar metabolism pathway significantly up-regulated the expression levels of related enzyme genes in glycolysis, tricarboxylic acid cycle (TCA), and oxidative phosphorylation processes after fruit disease onset. The response of plants to external environmental signaling pathways revealed a significant down-regulation of resistance enzyme gene expression, a significant up-regulation of pathogenic protein gene expression, and a significant down-regulation of resistance protein gene expression. The antioxidant pathway revealed significant down-regulation of glutathione synthesis gene expression, significant up-regulation of flavonoid biosynthesis related gene expression, significant down-regulation of L-ascorbate peroxidase (APX) gene expression, and significant up-regulation of L-ascorbate oxidase (AOX) homologous gene expression. RNA-Seq and RT-qPCR analysis indicated that pineapple tissue significantly up-regulated key genes in sugar metabolism to accelerate sugar metabolism in fruit disease part, significantly up-regulated key genes in the MAPK signaling pathway, and significantly down-regulated metabolic pathway changes such as antioxidant substances, leading to pineapple intern browning. The results could enrich the gene network of pineapple intern browning and provide a valuable reference for the subsequent gene screening of pineapple intern browning.

, authors=null, authorsList=Mengzhuo ZHANG, Qiting NA, Changsong ZHU, Hui CAO, Shiying LIU, Xuequn SHI, Lanhuan MENG, authorCompany=null, correspAuthors=Lanhuan MENG, 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=1277293257784693317, articleId=1277293254131454511, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=采后常温贮藏下菠萝罹病果实转录组测序分析, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

菠萝在常温贮藏过程中易发生黑心病,为了探索黑心病的发生机制,选取菠萝黑心病初期果实的发病部位和健康部位,每个部位选取3个样本分别进行测转录组RNA-Seq分析,对差异基因进行GO、KEGG、各代谢通路基因表达聚类分析和RT-qPCR验证,对比病部(IB)和健部(WT)的差异基因表达量。通过分析发现,IB vs WT共有1037个差异基因,其中上调886个,下调130个。GO和KEGG分析发现氨基酸生物合成差异基因最显著,而且差异基因数量占比大;通过聚类分析和RT-qPCR验证,糖代谢路径发现果实发病后糖酵解、三羧酸循环(TCA)和氧化磷酸化过程中相关酶基因表达量显著上调;植物应对外界环境信号通路发现抗性酶基因表达量显著下调,致病蛋白基因表达量显著上调,抗病蛋白基因表达量显著下调;抗氧化物质通路发现谷胱甘肽合成基因表达量显著下调,类黄酮生物合成相关基因表达量显著上调,L-抗坏血酸过氧化物酶(APX)基因表达量显著下调,而L-抗坏血酸氧化酶(AOX)同系物基因表达量显著上调。RNA-Seq和RT-qPCR分析结果表明,菠萝组织通过显著上调糖代谢关键基因加速果实病部糖代谢、显著上调表达信号传导关键通路MAPK途径中的关键基因以及显著下调抗氧化物质等代谢通路变化而导致黑心病的发生。通过这些结果可以丰富菠萝黑心病发生的基因网络,为后续菠萝黑心病相关基因筛选提供信息参考。

, authors=

张梦卓(1997—),女,博士研究生,研究方向:采后果蔬贮藏分子生物学。

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* 孟兰环(MENG Lanhuan),E-mail:
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张梦卓(1997—),女,博士研究生,研究方向:采后果蔬贮藏分子生物学。

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张梦卓(1997—),女,博士研究生,研究方向:采后果蔬贮藏分子生物学。

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Foods, 2022, 11(8): 1174., articleTitle=Metabolomic analysis, combined with enzymatic and transcriptome assays, to reveal the browning resistance mechanism of fresh-cut eggplant, refAbstract=null)], funds=[Fund(id=1277293270153695884, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, awardId=322QN252, language=CN, fundingSource=海南省自然科学基金项目(322QN252), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1277293258065711687, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, xref=null, ext=[AuthorCompanyExt(id=1277293258074100296, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, companyId=1277293258065711687, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=School of Food Science and Engineering, Hainan University, Haikou, Hainan 570228, China), AuthorCompanyExt(id=1277293258086683209, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, companyId=1277293258065711687, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=海南大学食品科学与工程学院,海南海口 570228)])], figs=[ArticleFig(id=1277293266362045045, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 1, caption=Disease and healthy parts of pineapple fruit, figureFileSmall=YoMkw6eHGe7Ivvzd+tfvdA==, figureFileBig=zShgrtP/0n+FejzRg987pg==, tableContent=null), ArticleFig(id=1277293266441736822, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图1, caption=菠萝果实病部和健部图, figureFileSmall=YoMkw6eHGe7Ivvzd+tfvdA==, figureFileBig=zShgrtP/0n+FejzRg987pg==, tableContent=null), ArticleFig(id=1277293266836001399, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 2, caption=Principal component analysis PCA (A), gene expression distribution box diagram (B) and Pearson correlation diagram (C) among different samples, figureFileSmall=9a0tFJsn7yOhTqOBtq82kA==, figureFileBig=SB4NY7W6QMpP4N/3m0Hw6A==, tableContent=null), ArticleFig(id=1277293267142185593, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图2, caption=不同样本间主成分分析(A)、基因表达分布盒型图(B)和Pearson相关性图(C), figureFileSmall=9a0tFJsn7yOhTqOBtq82kA==, figureFileBig=SB4NY7W6QMpP4N/3m0Hw6A==, tableContent=null), ArticleFig(id=1277293267230265978, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 3, caption=Number of differentially expressed genes between groups by Wayne diagram (A) and volcano diagram (B), figureFileSmall=3etiM3XfJDgXJQmytfa17A==, figureFileBig=lt5CJSOoOWXbsL6zVYtMCQ==, tableContent=null), ArticleFig(id=1277293267318346363, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图3, caption=组间差异表达基因数量韦恩图(A)和火山图(B), figureFileSmall=3etiM3XfJDgXJQmytfa17A==, figureFileBig=lt5CJSOoOWXbsL6zVYtMCQ==, tableContent=null), ArticleFig(id=1277293267377066620, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 4, caption=Go enrichment (A) and KEGG metabolic pathway (B), figureFileSmall=lyuuM4chs1PLAjydfXVXlQ==, figureFileBig=193Rvn+EMy24nCH0Uu6ITQ==, tableContent=null), ArticleFig(id=1277293267574198909, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图4, caption=GO富集(A)和KEGG代谢通路(B), figureFileSmall=lyuuM4chs1PLAjydfXVXlQ==, figureFileBig=193Rvn+EMy24nCH0Uu6ITQ==, tableContent=null), ArticleFig(id=1277293269184811647, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 5, caption=Biological oxidation process of glucose metabolism

A: The expression of glycolytic pathway and related enzymes; B: The expression of tricarboxylic acid cycle (TCA) metabolic pathway and related enzymes; C: The expression of oxidative phosphorylation pathway and related enzymes.

, figureFileSmall=h2VwpizSAd3TDdIOWAiD2Q==, figureFileBig=9Zdhy0qYV3XSG/qXVem0DQ==, tableContent=null), ArticleFig(id=1277293269260309120, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图5, caption=糖代谢的生物氧化过程

A:糖酵解通路及相关酶的表达;B:三羧酸循环(TCA)代谢通路及相关酶的表达;C:氧化磷酸化途径及相关酶的表达。

, figureFileSmall=h2VwpizSAd3TDdIOWAiD2Q==, figureFileBig=9Zdhy0qYV3XSG/qXVem0DQ==, tableContent=null), ArticleFig(id=1277293269344195201, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 6, caption=Heat map of signal pathway for plants to cope with external environment

A: The MAPK signal pathway of plants; B: The plant hormone signal pathway; C: The interaction of plant pathogens.

, figureFileSmall=v5KEmCQxTNATf6txgjwU7Q==, figureFileBig=LmAdRNbxwnZEngBm5K0l2A==, tableContent=null), ArticleFig(id=1277293269453247107, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图6, caption=植物应对外界环境的信号通路热图

A:植物MAPK信号通路;B:植物激素信号通路;C:植物病原相互作用。

, figureFileSmall=v5KEmCQxTNATf6txgjwU7Q==, figureFileBig=LmAdRNbxwnZEngBm5K0l2A==, tableContent=null), ArticleFig(id=1277293269532938884, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 7, caption=Heat map related to antioxidant substances

A: Phenylpropane biosynthesis; B: Glutathione metabolism; C: Ascorbic acid and aldonic acid metabolism; D: Flavonoid biosynthesis.

, figureFileSmall=k1T62UqIOTbYr5c2c+nL9w==, figureFileBig=u0vDC10zhL6EacEpfV64HA==, tableContent=null), ArticleFig(id=1277293269604242053, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图7, caption=抗氧化物质相关热图

A:苯丙烷生物合成;B:谷胱甘肽代谢;C:抗坏血酸和醛酸代谢;D:类黄酮生物合成。

, figureFileSmall=k1T62UqIOTbYr5c2c+nL9w==, figureFileBig=u0vDC10zhL6EacEpfV64HA==, tableContent=null), ArticleFig(id=1277293269662962310, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 8, caption=Expression of key genes in different pathways under disease and healthy of fruit

* and ** indicate significant difference (P<0.05, P<0.01); *** and **** indicate extremely significant difference (P<0.001, P<0.0001).

, figureFileSmall=6DWN5IjMIXz0rSfbgbaTVg==, figureFileBig=n2Rj24BQKo1f43xfjhx2dg==, tableContent=null), ArticleFig(id=1277293269730071175, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图8, caption=不同路径关键基因在果实病健部的表达量

*和**表示差异显著(P<0.05,P<0.01);***和****表示差异极显著(P<0.001,P<0.0001)。

, figureFileSmall=6DWN5IjMIXz0rSfbgbaTVg==, figureFileBig=n2Rj24BQKo1f43xfjhx2dg==, tableContent=null), ArticleFig(id=1277293269797180040, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Fig. 9, caption=Occurrence path of pineapple intern browning, figureFileSmall=4I9m9Anc9+4ijfPxOZsvRA==, figureFileBig=7Y+u4W1ThMMHgh6oY61LVQ==, tableContent=null), ArticleFig(id=1277293269860094601, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=图9, caption=菠萝黑心病发生路径, figureFileSmall=4I9m9Anc9+4ijfPxOZsvRA==, figureFileBig=7Y+u4W1ThMMHgh6oY61LVQ==, tableContent=null), ArticleFig(id=1277293269939786378, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=EN, label=Tab. 1, caption=

Specific primers used for qRT-PCR

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene引物序列(5ʹ-3ʹ)Primer sequence (5ʹ-3ʹ)
β-actinF: CTGGCCTACGTGGCACTTGACTT
R: CACTTCTGGGCAGCGGAACCTTT
109726387F: TCTAGATGAGAAGCGCCGTT
R: ACGTAGAACTTCTGGTGCCA
109726511F: TGGACAAGTACGAGCTCCTG
R: ACGACCTCTTTGAACCGGAT
109707674F: CTGAGAATGAACAGCTCGCC
R: GGTTATTGTGGTGAGCGCAT
109715689F: CGTGTTACTATGCATGGCCC
R: CAAACAGGTTCTCGCCGTAG
109715970F: CGATCTGCAGCTTTTCACGA
R: TGCAGAAGAGGCTCCATGAA
109722976F: AAGTTCATCCAGTACCGCCA
R: CTTGGTCTTGTTGCGGATCC
109727398F: CGTAAAGCACTTCTCGGTCG
R: CCTCGCAGTTGTCCATGATG
109709450F: TCAGCGATGAAGACCGATCA
R: GGACGATAAGAGGACGGGAG
109713066F: GCCAGAACCCAAGCAAAGAA
R: CCACCTCCTCATCCGTCAAT
109727686F: CTTCGAAGCCAACATCCTCG
R: GCTTCTTGGCCATCCTCATG
109725671F: GCGAAGTTTGTTGGGGAGTT
R: CTTGGACAATTTGCCTGGCT
109708431F: GGGGTGACGGGATTGTTAGA
R: CTGCATCAACCTCGACAGTG
109708663F: AATTTGGAACTTTGCGGCCT
R: TTGACCTCGGCACAAGTTTG
109727824F: TCGTCGCTGTAGAGATCACC
R: TGTATGCCCGCCAGATAGAG
109719227F: AAGTACAACCTCATCGCCGA
R: GTTGTACCCCTTCCTGCTCT
109719166F: TGGTGATGGTGGATGGAGTC
R: CAGCAAGCAGTGTTCCCTTT
109719641F: CGAGCACTTCTACAGGGACA
R: TAGAGAGCTGGAAGGGGAGT
109727857F: GCATCTTCGTCGACACCATC
R: CCACCAAACTCTCACCCTTC
109720628F: CTACTCCAACATCTGCGCCT
R: TCATTCTTCGGGCGTATCAGA
109728610F: TGTGGGATGCGCTCTACC
R: GCCTTTGCCCCAACACTG
109709714F: TCCGCTTCCAGATCCTTCTC
R: TCCACCATGTTGTTGCTGTG
109703559F: TGACATGGCTGAGCAACTTG
R: ATAACCGTGGCCTCAGGAAA
109710134F: CCACATGTTCGTCGTCAAGG
R: TCGTACATACCGTCGAGCTT
109708439F: CAATCCTGGTTCTGAGGGGT
R: CTCTGATCGTTGGCTGCTTC
109716911F: CCAAGGCTTGTTCCAGGATG
R: AGACCTCTAGCTCGACATGC
109723651F: ACTGGGGAGGGAATTGACTG
R: TTCGCCTGTCTCTTGGTCAT
109725790F: TCCTCAGCACACCCATCATT
R: CTGCCGTCGATCAATCTGTG
109706271F: AGCTGCGGAATCTCTACAGG
R: TCACGGGCTTTGTACACTCT
109710080F: AGTGTGGGTGGAGTGAGATG
R: TACGATGTGCTCCCCTTTGT
109720819F: TCCACTTCTCCGACCTCCTA
R:GTAGATGTGGAAGAGCGGGA
), ArticleFig(id=1277293270036255371, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1277293254131454511, language=CN, label=表1, caption=

实时荧光定量PCR的特异性引物

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene引物序列(5ʹ-3ʹ)Primer sequence (5ʹ-3ʹ)
β-actinF: CTGGCCTACGTGGCACTTGACTT
R: CACTTCTGGGCAGCGGAACCTTT
109726387F: TCTAGATGAGAAGCGCCGTT
R: ACGTAGAACTTCTGGTGCCA
109726511F: TGGACAAGTACGAGCTCCTG
R: ACGACCTCTTTGAACCGGAT
109707674F: CTGAGAATGAACAGCTCGCC
R: GGTTATTGTGGTGAGCGCAT
109715689F: CGTGTTACTATGCATGGCCC
R: CAAACAGGTTCTCGCCGTAG
109715970F: CGATCTGCAGCTTTTCACGA
R: TGCAGAAGAGGCTCCATGAA
109722976F: AAGTTCATCCAGTACCGCCA
R: CTTGGTCTTGTTGCGGATCC
109727398F: CGTAAAGCACTTCTCGGTCG
R: CCTCGCAGTTGTCCATGATG
109709450F: TCAGCGATGAAGACCGATCA
R: GGACGATAAGAGGACGGGAG
109713066F: GCCAGAACCCAAGCAAAGAA
R: CCACCTCCTCATCCGTCAAT
109727686F: CTTCGAAGCCAACATCCTCG
R: GCTTCTTGGCCATCCTCATG
109725671F: GCGAAGTTTGTTGGGGAGTT
R: CTTGGACAATTTGCCTGGCT
109708431F: GGGGTGACGGGATTGTTAGA
R: CTGCATCAACCTCGACAGTG
109708663F: AATTTGGAACTTTGCGGCCT
R: TTGACCTCGGCACAAGTTTG
109727824F: TCGTCGCTGTAGAGATCACC
R: TGTATGCCCGCCAGATAGAG
109719227F: AAGTACAACCTCATCGCCGA
R: GTTGTACCCCTTCCTGCTCT
109719166F: TGGTGATGGTGGATGGAGTC
R: CAGCAAGCAGTGTTCCCTTT
109719641F: CGAGCACTTCTACAGGGACA
R: TAGAGAGCTGGAAGGGGAGT
109727857F: GCATCTTCGTCGACACCATC
R: CCACCAAACTCTCACCCTTC
109720628F: CTACTCCAACATCTGCGCCT
R: TCATTCTTCGGGCGTATCAGA
109728610F: TGTGGGATGCGCTCTACC
R: GCCTTTGCCCCAACACTG
109709714F: TCCGCTTCCAGATCCTTCTC
R: TCCACCATGTTGTTGCTGTG
109703559F: TGACATGGCTGAGCAACTTG
R: ATAACCGTGGCCTCAGGAAA
109710134F: CCACATGTTCGTCGTCAAGG
R: TCGTACATACCGTCGAGCTT
109708439F: CAATCCTGGTTCTGAGGGGT
R: CTCTGATCGTTGGCTGCTTC
109716911F: CCAAGGCTTGTTCCAGGATG
R: AGACCTCTAGCTCGACATGC
109723651F: ACTGGGGAGGGAATTGACTG
R: TTCGCCTGTCTCTTGGTCAT
109725790F: TCCTCAGCACACCCATCATT
R: CTGCCGTCGATCAATCTGTG
109706271F: AGCTGCGGAATCTCTACAGG
R: TCACGGGCTTTGTACACTCT
109710080F: AGTGTGGGTGGAGTGAGATG
R: TACGATGTGCTCCCCTTTGT
109720819F: TCCACTTCTCCGACCTCCTA
R:GTAGATGTGGAAGAGCGGGA
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采后常温贮藏下菠萝罹病果实转录组测序分析
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张梦卓 , 纳琦婷 , 朱长松 , 曹慧 , 刘诗颖 , 史学群 , 孟兰环 *
热带作物学报 | 组学与生物技术 2024,45(11): 2287-2297
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热带作物学报 |组学与生物技术 2024 , 45 (11) : 2287 -2297
采后常温贮藏下菠萝罹病果实转录组测序分析
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张梦卓, 纳琦婷, 朱长松, 曹慧, 刘诗颖, 史学群, 孟兰环*
作者信息
  • 海南大学食品科学与工程学院,海南海口 570228
通讯作者:
* 孟兰环(MENG Lanhuan),E-mail:
Transcriptome Sequencing Analysis of Diseased Pineapple Fruits Stored at Room Temperature after Harvest
Mengzhuo ZHANG, Qiting NA, Changsong ZHU, Hui CAO, Shiying LIU, Xuequn SHI, Lanhuan MENG*
Affiliations
  • School of Food Science and Engineering, Hainan University, Haikou, Hainan 570228, China
出版时间: 2024-11-25 doi: 10.3969/j.issn.1000-2561.2024.11.006
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菠萝在常温贮藏过程中易发生黑心病,为了探索黑心病的发生机制,选取菠萝黑心病初期果实的发病部位和健康部位,每个部位选取3个样本分别进行测转录组RNA-Seq分析,对差异基因进行GO、KEGG、各代谢通路基因表达聚类分析和RT-qPCR验证,对比病部(IB)和健部(WT)的差异基因表达量。通过分析发现,IB vs WT共有1037个差异基因,其中上调886个,下调130个。GO和KEGG分析发现氨基酸生物合成差异基因最显著,而且差异基因数量占比大;通过聚类分析和RT-qPCR验证,糖代谢路径发现果实发病后糖酵解、三羧酸循环(TCA)和氧化磷酸化过程中相关酶基因表达量显著上调;植物应对外界环境信号通路发现抗性酶基因表达量显著下调,致病蛋白基因表达量显著上调,抗病蛋白基因表达量显著下调;抗氧化物质通路发现谷胱甘肽合成基因表达量显著下调,类黄酮生物合成相关基因表达量显著上调,L-抗坏血酸过氧化物酶(APX)基因表达量显著下调,而L-抗坏血酸氧化酶(AOX)同系物基因表达量显著上调。RNA-Seq和RT-qPCR分析结果表明,菠萝组织通过显著上调糖代谢关键基因加速果实病部糖代谢、显著上调表达信号传导关键通路MAPK途径中的关键基因以及显著下调抗氧化物质等代谢通路变化而导致黑心病的发生。通过这些结果可以丰富菠萝黑心病发生的基因网络,为后续菠萝黑心病相关基因筛选提供信息参考。

常温贮藏  /  菠萝  /  黑心病  /  RNA-Seq分析

Pineapple is prone to intern browning during storage at room temperature. Diseased and healthy parts of pineapple at early stage of intern browning were used to explore the mechanism of the disease. Three samples from each part were used for transcriptome RNA-Seq analysis. GO, KEGG, cluster analysis of gene expression in various metabolic pathways, and RT-qPCR validation on differential genes were performed and the differential gene expression levels between the diseased (IB) and healthy (WT) parts were compared. IB vs WT had 1037 differentially expressed genes, of which 886 were up-regulated and 130 were down-regulated. GO and KEGG analysis found that the differentially expressed genes in amino acid biosynthesis were the most significant, and the proportion of differentially expressed genes was large. Cluster analysis and RT-qPCR validation found that the sugar metabolism pathway significantly up-regulated the expression levels of related enzyme genes in glycolysis, tricarboxylic acid cycle (TCA), and oxidative phosphorylation processes after fruit disease onset. The response of plants to external environmental signaling pathways revealed a significant down-regulation of resistance enzyme gene expression, a significant up-regulation of pathogenic protein gene expression, and a significant down-regulation of resistance protein gene expression. The antioxidant pathway revealed significant down-regulation of glutathione synthesis gene expression, significant up-regulation of flavonoid biosynthesis related gene expression, significant down-regulation of L-ascorbate peroxidase (APX) gene expression, and significant up-regulation of L-ascorbate oxidase (AOX) homologous gene expression. RNA-Seq and RT-qPCR analysis indicated that pineapple tissue significantly up-regulated key genes in sugar metabolism to accelerate sugar metabolism in fruit disease part, significantly up-regulated key genes in the MAPK signaling pathway, and significantly down-regulated metabolic pathway changes such as antioxidant substances, leading to pineapple intern browning. The results could enrich the gene network of pineapple intern browning and provide a valuable reference for the subsequent gene screening of pineapple intern browning.

room temperature storage  /  pineapple  /  intern browning  /  RNA-Seq analysis
张梦卓, 纳琦婷, 朱长松, 曹慧, 刘诗颖, 史学群, 孟兰环. 采后常温贮藏下菠萝罹病果实转录组测序分析. 热带作物学报, 2024 , 45 (11) : 2287 -2297 . DOI: 10.3969/j.issn.1000-2561.2024.11.006
Mengzhuo ZHANG, Qiting NA, Changsong ZHU, Hui CAO, Shiying LIU, Xuequn SHI, Lanhuan MENG. Transcriptome Sequencing Analysis of Diseased Pineapple Fruits Stored at Room Temperature after Harvest[J]. Chinese Journal of Tropical Crops, 2024 , 45 (11) : 2287 -2297 . DOI: 10.3969/j.issn.1000-2561.2024.11.006
菠萝(Ananas comosus L.),属凤梨属,又名凤梨,仅次于香蕉和芒果的第三大热带水果,是世界四大名果之一[1-2]。原产于南美洲巴西、巴拉圭[3],现已在热带地区广泛种植。菠萝深受消费者喜爱,它风味独特,富含膳食纤维、有机酸、维生素B1、维生素C、类胡萝卜素、钾及多种矿物质等物质[4],其中菠萝蛋白酶是一种促消化和抗炎的物质[5-7]。中国的菠萝产地面积位居世界第4位,产量为世界第6位,虽然我国是菠萝生产和消费大国,但仍不是菠萝贸易强国[8-9]
菠萝黑心病(black heart),也称内部褐变病(internal browning, IB),是一种生理代谢失调病[10],一般从果实外部无法观察,切开果实才能发现。黑心病初发时,在果实基部的果心两侧出现水渍状斑点,之后斑点颜色变暗、范围变大;发展严重时,病斑联合一起,使大部分果肉褐变[11]。研究发现,果实内部褐变与酚类物质氧化成醌类、活性氧(reactive oxygen species, ROS)、膜脂过氧化等有关[12-13]。目前证明可延缓黑心病的方法包括氯化钙[14]、热诱导[15]、水杨酸[16]、1-甲基丙烯(1-methylcyclopropene, 1-MCP)[17-18]和打蜡协同效应[19]、外源抗坏血酸[20]等处理,但仍难以实现广泛应用,黑心病仍是影响菠萝商品价值和流通性的主要病害。
2015年福建农林大学首次破译了菠萝基因组[21],在菠萝基因组的研究取得了很大的进展,但目前多是对菠萝幼苗、花进行测序来研究果实生长发育[22-24],菠萝果实黑心病相关基因的研究甚少,仅发现AcPPO[25]AcGA2ox[26]AcCYS1[27]AcPLD2/9[28]等可能与黑心病相关,且其功能也未进行验证。
因此,我们对常温贮藏6 d发病初期果实的病部和健部进行转录组RNA-Seq分析,其主要包括:首先对测序结果进行总体数据可行性证明;然后对差异基因进行基因本体论(gene ontology, GO)基因功能注释和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)富集分析得到主要的代谢通路;最后对糖代谢、植物应对外界环境的信号通路和抗氧化物质相关通路进行差异基因聚类分析,可得到菠萝果实黑心病发生路径。本研究对黑心病如何发生有了更全面的了解,同时可得到一些相关基因,为今后通过分子手段控制黑心病发生提供新思路。
巴厘菠萝(Ananas comosus cv. Comtede Paris)于2021年10月采收于海南省琼海市,并于3 h内送至海南大学食品科学与工程学院采后果蔬保鲜实验室进行贮藏,挑选果实大小均一,无病害果实。果实贮藏于(25±1) ℃,相对湿度(RH)为(85±5)%环境。贮藏6 d后选取初期发病果实,取其病部和健部(图1),分别取3组,每组3个果实,迅速置于液氮中冻样,用干冰运输,送至天津诺禾致源科技有限公司进行有参转录组测序分析。健部(WT):C1、C2、C3,病部(IB):IB1、IB2、IB3
使用Agilent 2100 bio-analyzer精确检测RNA完整性和总量;然后构建文库,后进行质检;质检合格后上机进行Illumina测序。
首先对原始数据中质量较低的reads进行过滤,得到高质量的clean data。然后使用HISAT2 v2.0.5构建参考基因组的索引,并使用HISAT2 v2.0.5将配对末端clean reads与参照基因组比对;采用StringTie(1.3.3b)进行新基因预测;对于有生物学重复的样本,使用DESeq2(1.20.0)软件进行差异表达分析。通过clusterProfiler(3.8.1)软件进行差异表达基因的GO和KEGG富集分析。
首先,用天根多糖多酚RNA试剂盒提取菠萝果实病部和健部果实RNA;接着使用天根FastKing gDNA Dispelling RT SuperMix试剂盒反转录合成cDNA;最后利用网站https://primer3.ut.ee/设计特异性引物(表1),然后通过天根FastReal qPCR PreMix(SYBR Green)试剂盒进行PCR反应,反应程序:95 ℃预变性5 min;95 ℃变性10 s,60 ℃退火30 s,72 ℃延伸30 s,40个循环;最后72 ℃延伸10 min。按照2-ΔΔCt方法计算[29]
采用Graphpad prism 10.1软件对数据进行方差分析和相关性分析。
对各样本进行转录组数据质量评估发现,WT和IB组间的样本分散,组内3个样本聚集,表明样本间生物学重复好(图2A);盒型图(图2B)可直观地看到各样本的基因分布情况,每个样本从下往上可以看出基因分布越来越少。样本间相关性均大于0.8,组内相关性数值相近,组间相关性数值差值大(图2C),表明样本可靠,可用于后续分析。
差异基因数目分析发现,WT和IB组共有基因为14 586个(图3A);IB vs WT的差异表达基因有1037个,其中上调基因886个,下调基因130个,上调基因的数量远大于下调基因(图3B)。
GO分析发现(图4A),分子功能(molecular function, MF)显著性富集,其中辅酶结合(coenzyme binding)基因显著上调且差异基因数量最多;生物过程(biological process, BP)显著性次之,其中药物代谢过程(drug metabolism process)基因显著上调且差异基因数量最多;细胞成分(cellular components, CC)无显著性富集。
KEGG代谢通路中(图4B),氨基酸生物合成(amino acid biosynthesis)通路中基因表达差异倍数最高且差异基因数最多(22个),其次为苯丙氨酸、酪氨酸和色氨酸生物合成(biosynthesis of phenylalanine, tyrosine and tryptophan)(9个),氨基糖和核苷酸糖代谢(amino sugar and nucleotide sugar metabolism)(11个),苯丙烷类生物合成(phenylpropane biosynthesis)(9个)等。
菠萝是糖含量丰富的水果之一,有研究表明果实褐变会加速糖代谢,糖含量降低[30-31],对糖的3个生物氧化过程分析发现。首先,糖酵解中葡萄糖在有氧条件下丙酮酸激酶基因(109727427、109726650、109726809、109710080、109722348)表达上调生成烯醇式酮酸,之后在非酶促反应下生成丙酮酸;在无氧条件下,乳酸脱氢酶基因(109727043)表达上调生成乳酸,丙酮酸脱羧酶基因(109719677)表达上调生成乙醛,乙醇脱氢酶基因(109706271、109720821、109721267)上调表达生成乙醇(图5A)。
然后,糖酵解生成的丙酮酸可以通过丙酮酸激酶催化生成乙酰CoA进入三羧酸循环(tricarboxylic acid cycle, TCA)(图5B),其关键酶柠檬酸合酶基因(109710242、109708439、109710921、109724956)上调表达,异柠檬酸脱氢酶基因(109716911、109710820)上调表达,а-酮戊二酸脱氢酶基因(109723651、109725790)上调表达,表明机体会加速代谢以获取能量。
最后,在线粒体内膜糖、脂或氨基酸发生氧化磷酸化(图5C),共有5个系统。复合体Ⅰ中NADH-Q还原酶基因(109709714、109703559、109709706、109711193、109723703、109716813、109719455、109708116、109703616、109708945、109728114、109727605)上调表达;复合体Ⅱ中琥珀酸-Q还原酶基因(109710134)上调表达;复合体Ⅲ细胞色素还原酶基因(109726546、109728610、109723560)上调表达;复合体Ⅳ细胞色素氧化酶基因(109703608、109716203、109722390、109711772、109725159、109725842、109717914)上调表达;复合体ⅤATP合酶基因(109720628、109710804、109722176、109712983、109715104、109710439、109705107、109718567、109712204)上调表达。
综上,果实病部糖酵解、TCA和氧化磷酸化过程相关基因表达上调,与果实发病呈正相关。
MAPK主要与植物应对外界环境刺激和植物激素有关。几丁质酶可以参与植物发育调控和抗病性,IB vs WT几丁质酶基因(109713885)表达量上升;蛋白激酶参与调节机体复杂功能,丝氨酸、苏氨酸蛋白激酶基因(109726387、109726511)显著上调;过氧化氢酶基因(catalase, CAT)(109707674)显著下调表达(图6A)。
植物激素主要包括乙烯(ethylene, EI)、生长素(auxin, IAA)、赤霉素(gibberellin, GA)、脱落酸(abscisic acid, ABA)。研究已经表明植物激素代谢和相关的信号转导系统可能与褐变有关[32]。且研究发现脱落酸和赤霉素与植物褐变紊乱过程相关[33]。类脱落酸受体基因PYL5(109727857)显著上调,表明在果实病部感受ABA信号增强,会促进下游基因表达,开启ABA信号通路,调控植物抗逆性(图6B)。
研究发现活性氧(ROS)与植物病原相互作用有关[34],并且可能与黑心病发生相关。类致病相关蛋白基因PRB1-3(109715689)显著上调表达,类抗病蛋白基因RPM1(109715970)下调表达,表明果实发病后ROS增加,但呼吸爆发氧会消除ROS对细胞产生的毒害作用,呼吸爆发氧化酶同源蛋白(A、B、C和E)基因(109717636、109728108、109722976、109704560)都上调表达。其次,当植物细胞受到外界刺激后,机体会产生热休克蛋白来抵抗压力,热休克蛋白基因(109721392、109728698、109727398)下调表达;WRKY家族基因和植物抗性有关,当植物受到外界压力刺激后该家族基因会大量表达,转录因子WRKY26基因(109709450)上调表达;钙是一种细胞膜上的次级调节分子,类钙调素基因(109713066、109726233)也显著上调表达,表明机体在果实发病后会启动钙离子调节系统(图6C)。
次生代谢苯丙烷生物合成途径是酚类和黄酮类化合物等抗氧化物质合成途径,可抑制果实褐变。4-香豆酸-CoA连接酶参与催化类黄酮物质合成,其相关基因(109711909、109720819、109711565、109713679、109713578)上调表达,可能会加快催化类黄酮物质的合成(图7A);黄酮和异黄酮都是黄酮类化合物,都属于抗氧化物质。查尔酮合成酶(chalcone synthase, CHS)是将苯丙烷代谢途径引向黄酮类化合物的合成第一关键酶,但是CHS基因表达下调,可能影响类黄酮的生物合成。查尔酮异构化酶(chalcone isomerase, CHI)是进入异黄酮代谢的关键酶,CHI基因(109719166、109719641)上调表达,其基因表达量升高(图7C)。苯丙氨酸解氨酶(phenylalanine ammonia-lyase, PAL)是酚类物质合成的相关酶,PAL基因109727686显著下调表达,而109713835上调表达,但下调基因FPKM值远大于上调基因(图7A)。过氧化物酶(peroxidase, POD)基因中既有上调基因,也有下调基因(图7A),研究发现POD是一个双向酶,既可氧化[35],又可抗氧化[36]
谷胱甘肽是一种还原剂,参与机体氧化还原反应,抑制果实褐变。γ-谷氨酰环化转移酶基因(109725671、109724587)上调表达,而5-氧代脯氨酸酶基因(109708431)下调表达,γ-谷氨酰半胱氨酸合成酶基因(109708663)下调表达(图7B),果实发病后谷胱甘肽合成途径上相关酶基因表达量降低。
抗坏血酸是一种抗氧化物质,可抑制黑心病的发生。菠萝果实中抗坏血酸含量丰富,为47.8 mg/100 g[30],对抗坏血酸和醛酸代谢变化分析,发现L-抗坏血酸过氧化物酶(L-ascorbate peroxidase, APX)基因(109727824)显著下调表达,而且L-抗坏血酸氧化酶(L-ascorbate oxidase, AOX)同系物(109719227)显著上调表达(图7D),可能病部果实抗氧化酶能力下降。
为了验证转录组数据,从不同路径中筛选共30个关键基因,通过RT-qPCR对果实病部和健部果实的30个基因转录水平进行分析。结果表明,糖代谢路径中TCA循环、丙酮酸代谢和氧化磷酸化关键基因在果实病部均显著上调表达(图8A),表明果实发病后机体能量代谢旺盛。MAPK信号通路中苏氨酸蛋白激酶、致病蛋白脱落酸受体基因在果实病部显著上调表达,而抗性基因(如抗病基因和过氧化氢酶)显著下调表达(图8B)。抗氧化通路抗氧化酶PAL和APX在病部显著下调表达,氧化酶AOX显著上调表达(图8C),表明果实发病后的抗病能力下降。这些结果也与转录组数据一致。
菠萝果实内部容易发生黑心病,而且其发生是由多种原因造成的,通过RNA-Seq分析得到黑心病可能与多个代谢通路有关。当早期果实受到外界刺激时,可诱导呼吸爆发氧化酶和热激蛋白进行抵抗;发病后果实病部致病相关的蛋白基因显著上调表达,抗病蛋白基因显著下调表达,可导致果实内部ROS增加,但MAPK途径可以通过调节几丁质酶、蛋白激酶和过氧化氢酶来抑制ROS产生;转录因子WRKY可调节细胞膜上的Ca2+信号通路;菠萝果实糖含量高,发病后糖代谢在有氧和无氧条件下相关基因表达显著升高;脱落酸受体基因表达显著升高,促进下游基因表达,调控果实抗逆性;抗氧化通路中合成黄酮相关基因表达下调,但是异黄酮相关基因表达上调;合成谷胱甘肽相关基因下调,抗坏血酸和醛酸代谢通路中生成APX的相关基因显著下调表达,而AOX的相关基因显著上调表达(图9)。
本研究通过RNA-Seq分析菠萝黑心病发病的差异基因,获得参与菠萝黑心病发病基因的基因网络,筛选出菠萝黑心病相关的候选基因,以通过分子生物手段改善菠萝黑心病。
有研究表明,荔枝在成熟过程中会产生大量乙醛和乙酸,加速发酵过程[37]。通过糖酵解分析可知,糖酵解在无氧条件下生成乙醛和乙酸的酶表达量升高,有氧条件下糖酵解生成的丙酮酸可以进入TCA循环,同样TCA过程中关键酶基因表达量显著上调,同时果实发病后氧化磷酸化途径中多种酶基因表达量也发生显著上调,说明果实发病后植物细胞代谢加快,需要更多的能量。
MAPK途径与植物体免疫、应对环境压力和正常的生长发育[38-40]有关。果实发生黑心病后,抗性酶基因表达量显著下调。类脱落酸受体基因PYL5表达量显著升高,可能会调控植物抗逆性。研究发现,机体会在早期大量表达热休克蛋白和呼吸爆发氧化酶来抵抗外界刺激[41-42],菠萝病部致病蛋白基因显著上调表达。
果实品质劣变与抗氧化物质含量有关,鲜切茄子褐变会使抗氧化物质GSH、ASA含量降低[43]。果实发病后,抗氧化物质代谢通路谷胱甘肽合成基因表达下调,黄酮生物合成途径基因下调表达,L-抗坏血酸过氧化物酶(APX)基因显著下调表达,但L-抗坏血酸氧化酶同系物基因显著上调表达,总体来说,果实发病后相关抗氧化物质基因表达量降低,但氧化性物质基因表达量升高,这将会使果实衰老加速,病情恶化。
综上所述,本研究从RNA-Seq数据中选择3个与菠萝黑心病相关的路径,对其差异进行聚类和定量验证分析,发现菠萝果实发病后,病部糖酵解、TCA和生物氧化过程相关基因表达量显著上调、抗性蛋白基因表达显著下调,致病蛋白基因表达显著上调,抗氧化相关酶基因表达显著下调,氧化酶基因表达显著上调。通过上述分析可以选择与黑心病相关的候选基因,以丰富菠萝黑心病的基因网络。
  • 海南省自然科学基金项目(322QN252)
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doi: 10.3969/j.issn.1000-2561.2024.11.006
  • 接收时间:2024-04-11
  • 首发时间:2026-06-26
  • 出版时间:2024-11-25
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  • 收稿日期:2024-04-11
  • 修回日期:2024-05-13
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海南省自然科学基金项目(322QN252)
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    海南大学食品科学与工程学院,海南海口 570228

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* 孟兰环(MENG Lanhuan),E-mail:
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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

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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