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Article(id=1276190519453684092, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276190518317023323, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2024.05.002, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1690819200000, receivedDateStr=2023-08-01, revisedDate=1697299200000, revisedDateStr=2023-10-15, acceptedDate=null, acceptedDateStr=null, onlineDate=1782197130311, onlineDateStr=2026-06-23, pubDate=1716566400000, pubDateStr=2024-05-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782197130311, onlineIssueDateStr=2026-06-23, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782197130311, creator=13701087609, updateTime=1782197130311, updator=13701087609, issue=Issue{id=1276190518317023323, tenantId=1146029695717560320, journalId=1235980609244409860, year='2024', volume='45', issue='5', pageStart='873', pageEnd='1093', issueExtLink='null', onlineDate='null', pubDate='1716566400000', pubDateStr='2024-05-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782197130040, creator='13701087609', updateTime=1782197317472, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1276191304694493587, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276190518317023323, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1276191304694493588, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276190518317023323, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=886, endPage=893, ext={EN=ArticleExt(id=1276190520846193022, articleId=1276190519453684092, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Transcriptome Analysis of Lateral Petals of Oncidium and Mining of Transcription Factors Related to The Regulation of Labialization Variation, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Oncidium is an important fresh-cut flower in the market because of its unique flower pattern and brilliant color. The petals of Oncidium are highly susceptible to flower diversity. RNA extraction and transcriptome analysis were performed on the lateral petals of O. flexuosum ‘Honey Angel’ and variants with two lateral petals converted into lips to explore the molecular mechanism regulating the labialization of Oncidium lateral petals. A total of 45 525 415 high-quality reads were obtained from the sequencing results and 52 253 unigenes were identified. The seven databases of NR, Swissprot, PFAM, GO, NT, KO and KOG were used to annotate gene functions and annotated to 31 828, 23 174, 21 369, 21 367, 20 830, 10 523, 6465 unigenes. Upon expression comparison,3120 differential genes were obtained between O. flexuosum ‘Honey Angel’ and the mutant. A total of 1537 differentially expressed genes were annotated into three functional groups: biological processes, cellular components and molecular functions. KEGG functional enrichment analysis enriched 690 differentially expressed genes into different metabolic pathways, with the most genes enriched by metabolic pathway. To date, the study of lip formation in orchids has focused more on the MADS-box gene family, not only five significantly differentially expressed MADS-box genes were screened in this transcriptome data, but also other transcription factor such as NAC, TCP, MYB and WRKY that may be related to the lip formation in Oncidium were also discovered. RT-qPCR was used to verify the expression of key genes, and the quantitative results were consistent with RNA-seq data, most of the genes were highly expressed in the lip-like lateral petals, indicating that the genes may positively regulate the development of the lip of Oncidium. In summary, this study excavated a large number of key transcription factors involved in the variation of labialization in Oncidium, which would provide a certain reference for the study of the molecular mechanism and regulatory network of lip formation of orchid.

, authors=null, authorsList=Sixian ZENG, Rangcai YU, Yanping FAN, authorCompany=null, correspAuthors=Yanping FAN, 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=1276190522259673484, articleId=1276190519453684092, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=文心兰侧花瓣转录组分析与调控唇瓣化变异相关转录因子的挖掘, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

文心兰因其独特的花型和艳丽的颜色是市场上重要的鲜切花。文心兰花瓣极易产生花型多样性，为了探究调控文心兰侧花瓣唇瓣化的分子机制，对柠檬绿文心兰（Oncidium flexuosum ‘Honey Angel’）及其侧花瓣唇瓣化变异种（突变体）的侧花瓣进行RNA提取和转录组分析。测序结果共获得45 525 415个高质量reads，鉴定出52 253个unigenes。利用NR、Swissprot、PFAM、GO、NT、KO、KOG七大数据库分别进行基因功能注释，分别注释到31 828、23 174、21 369、21 367、20 830、10 523、6465条unigenes。经表达量比较，在柠檬绿文心兰和突变体之间获得差异表达基因3120条。GO功能富集分析显示，共有1537条差异表达基因注释到生物过程、细胞组分和分子功能3个功能群组。KEGG功能富集分析显示，将690个差异表达基因富集到不同的代谢通路，其中代谢途径富集的基因最多。兰花唇瓣器官发育的研究更多地集中在MADS-box基因家族中，在该转录组数据中不仅筛选到5个显著差异表达MADS-box基因家族成员，还挖掘到其他可能与文心兰唇瓣发育相关的NAC、TCP、MYB及WRKY等转录因子。运用RT-qPCR对这些转录因子基因进行表达量验证，定量结果与RNA-seq数据一致，且这些转录因子大部分在文心兰唇瓣化侧花瓣中具有高表达，说明其可能正向调控着文心兰唇瓣器官的发育。综上所述，本研究挖掘到大量参与文心兰唇瓣化变异的关键转录因子，为兰花唇瓣发育分子机制及调控网络研究提供参考依据。

, authors=

曾思娴（1999—），女，硕士研究生，研究方向：观赏植物生物技术。

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* 范燕萍（FAN Yanping），E-mail：。
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曾思娴（1999—），女，硕士研究生，研究方向：观赏植物生物技术。

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曾思娴（1999—），女，硕士研究生，研究方向：观赏植物生物技术。

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journalId=1235980609244409860, articleId=1276190519453684092, language=EN, label=Fig. 4, caption=KEGG enrichment pathway of DEG in Oncidium lateral petals, figureFileSmall=vEKTxiKN//YU05J1BlRWVQ==, figureFileBig=yQ5Wz+eZUyZp2e2pAOdDng==, tableContent=null), ArticleFig(id=1277241928521486442, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=CN, label=图4, caption=文心兰侧花瓣差异表达基因的KEGG富集通路, figureFileSmall=vEKTxiKN//YU05J1BlRWVQ==, figureFileBig=yQ5Wz+eZUyZp2e2pAOdDng==, tableContent=null), ArticleFig(id=1277241928584401003, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=EN, label=Fig. 5, caption=Evolutionary tree analysis for differentially expressed transcription factors of Oncidium lateral petals, figureFileSmall=CpgcvRw4Vzox6t7nQL00ig==, figureFileBig=69BDyPZ/uuzzAXSMFm8g6A==, tableContent=null), ArticleFig(id=1277241928643121260, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=CN, label=图5, caption=文心兰侧花瓣差异转录因子进化树分析, figureFileSmall=CpgcvRw4Vzox6t7nQL00ig==, figureFileBig=69BDyPZ/uuzzAXSMFm8g6A==, tableContent=null), ArticleFig(id=1277241928697647213, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=EN, label=Fig. 6, caption=RT-qPCR verification for differentially expressed genes in transcriptome of Oncidium lateral petals, figureFileSmall=3lZ7JobwCtUf9D2krYTdIg==, figureFileBig=RY9RliBQWvApAh9UlrdiZg==, tableContent=null), ArticleFig(id=1277241928773144686, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=CN, label=图6, caption=文心兰侧花瓣转录组差异基因RT-qPCR验证, figureFileSmall=3lZ7JobwCtUf9D2krYTdIg==, figureFileBig=RY9RliBQWvApAh9UlrdiZg==, tableContent=null), ArticleFig(id=1277241928836059247, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=EN, label=Tab. 1, caption=

Differentially expressed transcription factors associated with labialization variation in Oncidium lateral petals

, figureFileSmall=null, figureFileBig=null, tableContent=
基因ID Gene ID标签Annotation功能基因DescriptionLog2(fold change)
Cluster-10510.4816ADJ67237.1MADS1；MADS box transcription factor 113.467
Cluster-10510.1587ADJ67240.1MADS10；MADS box transcription factor 106.4071
Cluster-10510.27791ADJ67241.1MADS11；MADS box transcription factor 111.8286
Cluster-10510.12679ADJ67239.1MADS7；MADS box transcription factor 7–1.1659
Cluster-10510.13070ADJ67234.1MADS5；MADS box transcription factor 5–2.5449
Cluster-10510.24492AVO00700.1WRKY1；WRKY transcription factor 28-like–2.1117
Cluster-10510.12328ATU32558.1TCP1；TCP-like protein1.3815
Cluster-10510.9271ATU32522.1TCP2；TCP1-like protein1.3949
Cluster-10510.1026XP_020697724.1NAC1；NAC domain-containing protein2.4272
Cluster-10510.15575PKU72007.1MYB1；Myb-related protein 305–6.3881
), ArticleFig(id=1277241928890585200, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276190519453684092, language=CN, label=表1, caption=

文心兰唇瓣化侧花瓣变异差异表达转录因子

, figureFileSmall=null, figureFileBig=null, tableContent=
基因ID Gene ID标签Annotation功能基因DescriptionLog2(fold change)
Cluster-10510.4816ADJ67237.1MADS1；MADS box transcription factor 113.467
Cluster-10510.1587ADJ67240.1MADS10；MADS box transcription factor 106.4071
Cluster-10510.27791ADJ67241.1MADS11；MADS box transcription factor 111.8286
Cluster-10510.12679ADJ67239.1MADS7；MADS box transcription factor 7–1.1659
Cluster-10510.13070ADJ67234.1MADS5；MADS box transcription factor 5–2.5449
Cluster-10510.24492AVO00700.1WRKY1；WRKY transcription factor 28-like–2.1117
Cluster-10510.12328ATU32558.1TCP1；TCP-like protein1.3815
Cluster-10510.9271ATU32522.1TCP2；TCP1-like protein1.3949
Cluster-10510.1026XP_020697724.1NAC1；NAC domain-containing protein2.4272
Cluster-10510.15575PKU72007.1MYB1；Myb-related protein 305–6.3881
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文心兰侧花瓣转录组分析与调控唇瓣化变异相关转录因子的挖掘
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曾思娴 1, 3 , 余让才 1, 3 , 范燕萍 2, 3, *
热带作物学报 | 组学与生物技术 2024,45(5): 886-893
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热带作物学报 |组学与生物技术 2024 , 45 (5) : 886 -893
文心兰侧花瓣转录组分析与调控唇瓣化变异相关转录因子的挖掘
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曾思娴（1999—），女，硕士研究生，研究方向：观赏植物生物技术。

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曾思娴1, 3, 余让才1, 3, 范燕萍2, 3, *
作者信息
  • 1.华南农业大学生命科学学院，广东广州　510642
  • 2.华南农业大学林学与风景园林学院，广东广州　510642
  • 3.华南农业大学花卉研究中心，广东广州　510642
通讯作者:
* 范燕萍（FAN Yanping），E-mail：。
Transcriptome Analysis of Lateral Petals of Oncidium and Mining of Transcription Factors Related to The Regulation of Labialization Variation
Sixian ZENG1, 3, Rangcai YU1, 3, Yanping FAN2, 3, *
Affiliations
  • 1.College of Life Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
  • 2.College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong 510642, China
  • 3.Flower Research Center, South China Agricultural University, Guangzhou, Guangdong, 510642, China
出版时间: 2024-05-25 doi: 10.3969/j.issn.1000-2561.2024.05.002
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摘要
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文心兰因其独特的花型和艳丽的颜色是市场上重要的鲜切花。文心兰花瓣极易产生花型多样性，为了探究调控文心兰侧花瓣唇瓣化的分子机制，对柠檬绿文心兰（Oncidium flexuosum ‘Honey Angel’）及其侧花瓣唇瓣化变异种（突变体）的侧花瓣进行RNA提取和转录组分析。测序结果共获得45 525 415个高质量reads，鉴定出52 253个unigenes。利用NR、Swissprot、PFAM、GO、NT、KO、KOG七大数据库分别进行基因功能注释，分别注释到31 828、23 174、21 369、21 367、20 830、10 523、6465条unigenes。经表达量比较，在柠檬绿文心兰和突变体之间获得差异表达基因3120条。GO功能富集分析显示，共有1537条差异表达基因注释到生物过程、细胞组分和分子功能3个功能群组。KEGG功能富集分析显示，将690个差异表达基因富集到不同的代谢通路，其中代谢途径富集的基因最多。兰花唇瓣器官发育的研究更多地集中在MADS-box基因家族中，在该转录组数据中不仅筛选到5个显著差异表达MADS-box基因家族成员，还挖掘到其他可能与文心兰唇瓣发育相关的NAC、TCP、MYB及WRKY等转录因子。运用RT-qPCR对这些转录因子基因进行表达量验证，定量结果与RNA-seq数据一致，且这些转录因子大部分在文心兰唇瓣化侧花瓣中具有高表达，说明其可能正向调控着文心兰唇瓣器官的发育。综上所述，本研究挖掘到大量参与文心兰唇瓣化变异的关键转录因子，为兰花唇瓣发育分子机制及调控网络研究提供参考依据。

文心兰  /  唇瓣化  /  转录组测序  /  差异表达基因

Oncidium is an important fresh-cut flower in the market because of its unique flower pattern and brilliant color. The petals of Oncidium are highly susceptible to flower diversity. RNA extraction and transcriptome analysis were performed on the lateral petals of O. flexuosum ‘Honey Angel’ and variants with two lateral petals converted into lips to explore the molecular mechanism regulating the labialization of Oncidium lateral petals. A total of 45 525 415 high-quality reads were obtained from the sequencing results and 52 253 unigenes were identified. The seven databases of NR, Swissprot, PFAM, GO, NT, KO and KOG were used to annotate gene functions and annotated to 31 828, 23 174, 21 369, 21 367, 20 830, 10 523, 6465 unigenes. Upon expression comparison,3120 differential genes were obtained between O. flexuosum ‘Honey Angel’ and the mutant. A total of 1537 differentially expressed genes were annotated into three functional groups: biological processes, cellular components and molecular functions. KEGG functional enrichment analysis enriched 690 differentially expressed genes into different metabolic pathways, with the most genes enriched by metabolic pathway. To date, the study of lip formation in orchids has focused more on the MADS-box gene family, not only five significantly differentially expressed MADS-box genes were screened in this transcriptome data, but also other transcription factor such as NAC, TCP, MYB and WRKY that may be related to the lip formation in Oncidium were also discovered. RT-qPCR was used to verify the expression of key genes, and the quantitative results were consistent with RNA-seq data, most of the genes were highly expressed in the lip-like lateral petals, indicating that the genes may positively regulate the development of the lip of Oncidium. In summary, this study excavated a large number of key transcription factors involved in the variation of labialization in Oncidium, which would provide a certain reference for the study of the molecular mechanism and regulatory network of lip formation of orchid.

Oncidium  /  labialization  /  transcriptome sequencing  /  differentially expressed genes
曾思娴, 余让才, 范燕萍. 文心兰侧花瓣转录组分析与调控唇瓣化变异相关转录因子的挖掘. 热带作物学报, 2024 , 45 (5) : 886 -893 . DOI: 10.3969/j.issn.1000-2561.2024.05.002
Sixian ZENG, Rangcai YU, Yanping FAN. Transcriptome Analysis of Lateral Petals of Oncidium and Mining of Transcription Factors Related to The Regulation of Labialization Variation[J]. Chinese Journal of Tropical Crops, 2024 , 45 (5) : 886 -893 . DOI: 10.3969/j.issn.1000-2561.2024.05.002
正文
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兰科植物因其独特的花型倍受人们喜爱，MADS-box转录因子是花的起始和发育过程中的关键调控成分，在参与花器官的发育、开花时间的调节等过程中均起着重要作用[1]。ABCDE模型由MADS-box基因家族中的五类同源基因组成，这些基因通过相互作用共同决定花器官身份[2]。因此，大多数关于兰花花器官发育的研究都集中在这些ABCDE基因上，而关于调控兰花唇瓣发育的其他转录因子及下游相关调控网络仍不清晰，因此，探究其他相关调控机制对兰花植物分子育种具有重要意义。
文心兰是兰科文心兰属植物，因其独特的花型和艳丽的颜色是世界上具有较高观赏价值的切花品种[3]。在长期的文心兰生长进化过程中，极易产生花型多样性，这种花型多样性主要体现在唇瓣的变化上，使其具有更高的观赏价值和生物学价值[4]。因此揭示文心兰唇瓣多样性形成机制显得极其重要。“花被密码模型”是目前被广泛接受的兰花花器官发育模型，该模型中，不同MADS-box基因分别组成唇瓣复合物和萼片/花瓣复合物，这2种蛋白复合物相互竞争决定兰花花器官身份形成[5]，而文心兰花瓣形态结构多样化的其他调控网络研究仍鲜有报道。本研究以柠檬绿文心兰（Oncidium. flexuosum‘Honey Angel’）和其侧花瓣唇瓣化变异种（突变体）为材料，对2种侧花瓣进行RNA转录组测序，通过MADS-box及其他转录因子的差异表达挖掘调控文心兰唇瓣化变异关键转录因子，为建立文心兰唇瓣化变异调控关系网络，培育花型独特兰花新品种奠定基础。
1　材料与方法
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1.1　材料
供试材料为种植在华南农业大学花卉研究中心种质资源圃中生长健壮的柠檬绿文心兰侧花瓣发生唇瓣化变异种（突变体），对照为柠檬绿文心兰（图1）。对2种侧花瓣表皮细胞观察，发现在8 mm花蕾时期表皮细胞数目差异最大，因此在9月和10月采集8 mm花蕾并分离其侧花瓣迅速置于液氮中冻存，然后保存于–80 ℃冰箱，用于后续转录组测序及相关试验。
1.2　方法
1.2.1　总RNA提取、文库构建与转录组测序
（1）总RNA提取。使用天根多糖多酚试剂盒（QIAGEN，Germany）提取柠檬绿文心兰和唇瓣化变异种的侧花瓣组织样品的总RNA，并检测其总量和完整性。RNA提取与检测均委托北京诺禾致源科技股份有限公司完成。
（2）文库构建、质检与测序。选取符合质量标准的总RNA通过Oligo（dT）磁珠富集带有polyA尾的mRNA。随后在NEB Fragmentation Buffer中用二价阳离子将得到的mRNA随机打断，按照NEBNext® Ultra™ RNA Library Prep Kit for Illumina®试剂盒说明书进行cDNA文库的构建。文库构建完成后，使用Qubit 2.0 Fluorometer荧光分光光度计进行初步定量，随后使用Agilent 2100 bioanalyzer生物分析仪对文库的insert size进行检测，通过RT-qPCR对文库有效浓度进行准确定量，以保证文库质量。把不同文库按照有效浓度及目标下机数据量的需求pooling后，使用Illumina NovaSeq 6000（Illumina，USA）测序平台进行转录组测序。
1.2.2　测序数据分析
（1）数据质控与转录本拼接。为了保证数据分析的质量和可靠性，将测序获得的原始数据（raw reads）进行过滤，去除带接头reads、含N碱基的reads、低质量reads（Q值<20），经过原始数据过滤、测序错误率检查、GC含量分布检查，获得后续分析使用的高质量clean reads。使用Trinity程序将clean reads进行拼接，对拼接获得的转录本去除冗余以Corset层次聚类后得到最长Cluster序列进行后续分析。
（2）unigene功能注释。得到拼接转录本后，将转录本通过NCBI Blastx后比对到蛋白质的7个数据库[Nr、Nt、Pfam、KOG、Swissprot、KEGG、GO，（E-value≤0.000001）]，获得与目标序列相似度最高的蛋白质，并对其unigenes进行功能注释。
1.2.3　差异表达基因筛选及富集分析
利用RSEM（RNA-seq by Expectation Maximization）软件[6]对基因在不同样本之间进行定量分析，并使用DESeq2软件对原始的read count进行标准化处理，通过统计学模型进行假设检验概率（P-value）计算后进行FDR矫正获得padj值。为了得到显著差异表达基因，将筛选条件设为padj<0.005且差异倍数|log2（fold change）|>1。分别使用GOseq[7]和KOBAS软件进行差异表达基因的GO和KEGG的富集分析，当padj<0.05时，为显著富集。
1.2.4　差异表达基因的RT-qPCR验证
以柠檬绿文心兰及其唇瓣化变异种为材料，基于转录组数据分析，筛选出与唇瓣变异相关的差异转录因子基因进行RT-qPCR验证。提取8 mm花蕾期柠檬绿和唇瓣化变异种文心兰的侧花瓣的RNA，利用湖南艾克瑞生物工程有限公司的Evo M-mlV反转录试剂盒合成cDNA单链。利用Primer Premier 5.0软件设计引物，委托上海生物工程有限公司合成引物。RT-qPCR反应体系和程序按照Hieff® qPCR SYBR Green Master Mix（Low Rox Plus）试剂盒操作说明进行，参考文心兰属植物相关研究以Actin为内参基因[8]，通过Applied Biosystems ABI7500荧光定量PCR仪检测10个相关转录因子基因的相对表达量，每个样品设置3个生物学重复，反应结束后确认扩增曲线和熔解曲线，使用2-ΔΔCT法计算相关基因在不同样品中的表达情况。
2　结果与分析
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2.1　转录组测序质量分析
取柠檬绿文心兰和唇瓣化变异种8 mm花蕾时期侧花瓣进行转录组测序。测序共获得46 436 745个raw reads，原始数据过滤后获得45 525 415个高质量clean reads。经质量评估，数据整体测序错误率不超过0.03%，Q20碱基百分比（测序错误率不小于1%）分布在96.61%~98%之间，Q30（测序错误率小于0.1%）介于91.63%~94.25%之间，GC含量介于45.92%~46.67%之间，表明测序质量较好，可用于后期数据分析。
2.2　转录组unigenes功能注释
将高质量clean reads进行拼接后共获得52 253个unigenes，利用NR、Swissport、PFAM、GO、NT、KO、KOG等7个常用蛋白质数据库进行比对及基因功能注释，根据比对蛋白数据库的序列同源性结果可知，至少在1个数据库注释成功的unigenes有36 118，占69.12%，其中与NR数据库匹配的unigenes数目最多为31 828条，占60.91%；其次为Swissport数据库23 174条（占44.34%），PFAM数据库21 369条（占40.89%），GO数据库21 367条（占40.89%），NT数据库20 830条（占39.86%），KO数据库10 523条（占20.13%），KOG数据库6465条（占12.37%）；在以上7个数据库中都注释成功的unigenes数目为3549条，占6.79%。
2.3　文心兰侧花瓣差异表达基因分布
对2种侧花瓣的unigenes表达量进行比较，以|log2（fold change）|≥1且padj<0.05作为筛选基准，在2种侧花瓣中共检测到差异表达基因（differentially expressed gene，DEG）3120条，其中与柠檬绿文心兰相比，在突变体侧花瓣中上调表达的DEG有1526条，下调表达的DEG有1594条（图2）。
2.4　差异表达基因的GO功能分析
将检测到的DEG进行GO功能富集分析，以注释其生物学功能。共有1537条差异表达基因注释到细胞组分（cellular component，CC）、生物学过程（biological process，BP）和分子功能（molecular function，MF）3个功能群组。其中差异表达基因更多富集在生物学过程功能中，主要途径包括生物学过程功能中的碳水化合物代谢过程（carbohydrate metabolic process）、脂质代谢过程（lipid metabolic process）和含核碱基化合物分解代谢过程（nucleobase-containing compound catabolic process）；在细胞组分功能上，主要富集在核质（nucleoplasm）和染色体（chromosome）中；分子功能中差异基因重点富集在氧化还原酶活性（oxidoreductase activity）和裂解酶活性（lyase activity）上（图3）。
2.5　差异表达基因的KEGG富集分析
将差异表达的基因进行KEGG富集分析，结果发现在2种侧花瓣中有690个差异表达的基因在KEGG途径中显著富集，KEGG富集的前20个途径如图4所示，其中代谢途径（metabolic pathways）、次生代谢物的生物合成（biosynthesis of secondary metabolites）和抗生素生物合成（biosynthesis of antibiotics）是富集差异表达基因个数较多的通路。
2.6　文心兰唇瓣化变异相关基因的挖掘与分析
MADS-box基因是一类广泛存在于植物中且被证明在兰花花器官发育中具有极其重要的调控作用。为了挖掘文心兰唇瓣化变异相关调控基因，首先从差异表达基因中重点关注MADS-box转录因子，在该转录组中共挖掘5个存在显著差异（以|log2（fold change）|>1为筛选依据）的MADS-box基因（MADS1、MADS10、MADS11、MADS7、MADS5）。在植物中MADS-box基因主要通过调节其他基因的转录来发挥作用[9]。因此，也对文心兰的侧花瓣转录组测序结果进行其他转录因子的数据分析，发现存在差异表达的其他转录因子主要包括WRKY、TCP、NAC、MYB等（表1）。
将MADS1、MADS10、MADS11、MADS7、MADS5、TCP1、TCP2、NAC1、MYB1蛋白与其他物种同源蛋白序列构建进化树，结果表明，MADS-box蛋白与扇叶文心兰（Erycina pusilla）的MADS-box亲缘关系最近，聚为一类，其次与铁皮石斛（Dendrobium catenatum）亲缘关系较近；NAC与铁皮石斛（Dendrobium catenatum）、蝴蝶兰（Phalaenopsis equestris）亲缘关系较近，聚为一类；TCP与蝴蝶兰（Phalaenopsis equestris）、蕙兰（Cymbidium faberi）亲缘关系最近，聚为一类；MYB与建兰（Cymbidium ensifolium）亲缘关系最近，聚为一类，其次与扇叶文心兰（Erycina pusilla）、铁皮石斛（Dendrobium catenatum）亲缘关系较近（图5）。
2.7　转录组测序RT-qPCR验证
为了验证文心兰侧花瓣转录组测序数据的真实性，共选择10个差异表达基因，通过RT-qPCR的方法检测其在花蕾期阶段的侧花瓣中的表达水平，与转录组测序获得的基因表达水平相比，二者变化趋势一致（图6），说明本研究的转录组测序结果具有良好的可靠性。
3　讨论
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本研究对柠檬绿文心兰和其侧花瓣唇瓣化变异种花蕾期侧花瓣进行RNA测序和转录组分析，共获得52 253个unigenes。利用NR、Swissprot、PFAM、GO、NT、KO、KOG七个数据库分别进行基因功能注释，分别注释到31 828（60.91%）、23 174（44.34%）、21 369（40.89%）、21 367（40.89%）、20 830（39.86%）、10 523（20.13%）、6465（12.37%）条unigenes，说明本转录组测序数据质量较高，为文心兰唇瓣发育相关研究及其分子育种提供理论基础。
检测到差异表达基因3120条，与柠檬绿文心兰相比，在突变体侧花瓣中上调基因有1526条，下调基因有1594条。其中1537条差异表达基因经GO功能富集分析注释到生物过程、细胞组分和分子功能3个功能群组，经KEGG功能富集主要分布在代谢途径、次生代谢物生物合成途径等。表明文心兰唇瓣化变异是一个复杂的过程，涉及多条代谢通路并受多种转录因子基因共同协调影响。
现有的研究揭示了MADS-box基因尤其是B类MADS-box基因在兰花花器官中的重要作用[10]。同时，同源性兰花Tepal（HOT）模型可以解释兰花MADS-box基因如何调控花器官的发育并推测B类基因中的不同基因与其他类别的MADS-box基因结合，以调节萼片、侧花瓣和唇瓣身份的复杂性[11]。截至目前，B类MADS-box基因通过基因复制事件产生大量同源基因，有学者从南茜文心兰中分离到4个B类MADS-box基因（OMADS3、OMADS5、OMADS8和OMADS9），这些基因相互作用形成同源或异源二聚体共同参与调控花被器官的形成，当OMADS5缺失而OMADS9存在时会导致大唇瓣以及萼片/侧花瓣唇瓣化突变体的产生[12]。除了B类MADS-box基因，“花被密码”模型认为B类AP3基因与E类AGL6基因相互组成萼片/侧花瓣复合物和唇瓣复合物，这2种蛋白复合物相互竞争调控着兰花复杂花被器官的形成[5]。在蝴蝶兰唇状花瓣突变体中，B类MADS-box基因（PeMADS4）在3个唇瓣状花瓣中具有明显的表达差异[13]，说明B类MADS-box基因在蝴蝶兰唇瓣发育中具有重要调控作用。此外，建兰花器官类型非常多样，并通过形态学观察和转录组分析发现其花型突变体与MADS-box基因的异常表达有关。在建兰唇状花瓣突变体以及唇状萼片突变体中，CeAP3-3、CeAP3-4和CeAGL6-2基因的高表达导致了这种唇瓣突变表型[14]。上述研究结果进一步证实了“花被密码”模型及该模型在兰科植物的广泛适应性。本研究通过对柠檬绿文心兰和其唇瓣化变异种的侧花瓣进行转录组测序，从差异基因中筛选到5个差异表达MADS-box基因MADS1、MADS10、MADS11、MADS7、MADS5，其中MADS5为B类基因且在突变体侧花瓣中下调表达，这与在南茜文心兰中该基因负向调控唇瓣器官的形成结果一致，推测其可能参与组成文心兰萼片/侧花瓣复合物促进柠檬绿文心兰正常花瓣的形成。MADS1、MADS10、MADS11、MADS7为E类基因且在突变体侧花瓣中上调表达（除MADS7），大量研究已经证实MADS1（AGL6-2）参与唇瓣复合物组成并促进文心兰大唇瓣、蝴蝶兰唇瓣状花瓣突变体及建兰花瓣/萼片唇瓣化突变体的产生[13-15]，其他E类基因是否同样参与唇瓣复合物的组成，或与其他调控元件一起共同参与文心兰唇瓣器官的发育还需要通过大量实验进一步证实。
尽管已有研究表明，MADS-box转录因子在兰花花瓣及唇瓣多样性的形成上扮演着重要的角色，但该基因家族是如何调控兰花唇瓣多样性形成机理尚不清楚。花器官身份基因的下游靶基因是花器官发生的关键调节因子，直接或间接作用于花器官组织[16]。通过高通量测序数据及整合多种生物学数据可以推断出相关的基因表达调控网络。因此，本研究也对转录组中差异表达的其他转录因子进行分析，发现NAC、TCP、MYB、WRKY等转录因子在文心兰唇瓣发育过程中存在差异表达。有研究发现，在玫瑰花瓣中NAC转录因子控制花朵花瓣中乙烯调节的细胞扩张，为NAC转录因子的功能提供新见解[17]。在小兰屿蝴蝶兰中，挖掘到PeNAC67是调控小兰屿蝴蝶兰唇瓣发育的关键转录因子，且该基因与唇瓣发育相关的MADS3基因存在互作，揭示了兰花唇瓣发育的分子机制[18]。将蝴蝶兰TCP转录因子PhCYCs基因在夏堇中进行异源表达，发现蝴蝶兰PhCYCs基因在夏堇中能正常转录，且所有转基因株系分株增多且花型改变，初步说明蝴蝶兰TCP转录因子可能既参与花型发育又调控分枝过程[19]。植物MYB转录因子除了在调控植物花青素生物合成上有重要贡献外，也有研究发现该基因家族在水稻中会调控花器官和小穗的分化[20]，而该转录因子在花卉植物花器官形成的相关调控作用尚未见报道。本研究通过转录组分析鉴定出的这些可能调控文心兰唇瓣发育的其他转录因子基因是否会与MADS-box转录因子相互作用共同调控文心兰唇瓣器官的发育仍需要通过大量实验进一步深入研究，以确定其具体功能和调控方式。
因此，本研究对唇瓣化变异文心兰侧花瓣进行转录组分析，获得了大量差异表达转录因子，为深入阐明这些转录因子的功能，完善文心兰唇瓣发育相关调控网络及分子机理奠定基础。
基金
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  • 全国农业科技现代化先行县建设项目（从化区）
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doi: 10.3969/j.issn.1000-2561.2024.05.002
  • 接收时间：2023-08-01
  • 首发时间：2026-06-23
  • 出版时间：2024-05-25
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  • 收稿日期：2023-08-01
  • 修回日期：2023-10-15
基金
全国农业科技现代化先行县建设项目（从化区）
作者信息
    1.华南农业大学生命科学学院，广东广州　510642
    2.华南农业大学林学与风景园林学院，广东广州　510642
    3.华南农业大学花卉研究中心，广东广州　510642

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* 范燕萍（FAN Yanping），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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