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畲药十二时辰基源植物重瓣铁线莲的全长转录组分析

何舒澜 柯兰兰 陈观水

何舒澜,柯兰兰,陈观水. 畲药十二时辰基源植物重瓣铁线莲的全长转录组分析 [J]. 福建农业学报,2024,39(9):1−10
引用本文: 何舒澜,柯兰兰,陈观水. 畲药十二时辰基源植物重瓣铁线莲的全长转录组分析 [J]. 福建农业学报,2024,39(9):1−10
HE S L, KE L L, CHEN G S. Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don [J]. Fujian Journal of Agricultural Sciences,2024,39(9):1−10
Citation: HE S L, KE L L, CHEN G S. Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don [J]. Fujian Journal of Agricultural Sciences,2024,39(9):1−10

畲药十二时辰基源植物重瓣铁线莲的全长转录组分析

基金项目: 福建省职业院校教师教学创新团队立项建设项目;福建省大学生创新创业项目(S202110389044);福建卫生职业技术学院教学创新团队专项(JG2021103)
详细信息
    作者简介:

    何舒澜(1980 —),男,硕士,副教授,主要从事中草药栽培与鉴定研究,E-mail: 181329113@qq.com

    通讯作者:

    陈观水(1979 —),男,博士,副教授,主要从事药用植物次生代谢研究,E-mail: gshchenfafu@163.com

  • 中图分类号: S 68

Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don

  • 摘要:   目的  重瓣铁线莲是畲药十二时辰基源植物,以根入药,含有丰富的活性成分,本研究旨在了解重瓣铁线莲基因注释信息,次级代谢产物代谢通路及基因功能,丰富其转录组信息,为进一步筛选和鉴定其药用成分代谢通路相关基因奠定基础。  方法  利用-SMRT测序技术,对重瓣铁线莲根进行全长转录组测序,并借助生物信息学工具进行功能注释、结构分析以及萜类合成途径基因的挖掘。  结果  测序共获得高质量测序subreads数据量为62.21 Gb,通过数据处理分析,获到20540条高质量去冗余转录本。利用NR, GO, NT, Pfam, COG/KOG, SwissProt, KEGG等7个数据库对高质量去冗余序列进行基因功能注释,共有19909条转录本至少在1个数据库得到注释,有8888条转录本在NR、NT、COG/KOG、KEGG、GO等5个公共数据库中均有注释。GO注释结果显示,14911条转录本共富集在包含生物学过程、细胞组成和分子功能三大类的53个条目中。KEGG分析显示,19701条转录本序列被富集到6条主通路和44条子通路。COG/KOG注释发现,13204条转录本被注释,其中注释最多的功能类别为一般功能预测。对转录本结构分析发现,共预测到978个转录因子、224条LncRNA、7167个SSR。对萜类化合物生物合成途径进行挖掘,共鉴定到48个转录本(16个关键酶候选基因)参与萜类骨架生物合成。  结论  本研究成功对畲药十二时辰基源植物重瓣铁线莲的根进行了全长转录组测序,获得了该物种的全长转录组相关基因功能信息,填补了重瓣铁线莲的基因信息缺乏的问题,为深入研究重瓣铁线莲的调控网络、生物学特征、相关代谢途径、信号通路及分子机制等提供参考。
  • 图  1  重瓣铁线莲转录本在七大数据库注释结果

    Figure  1.  Annotation results of transcripts in seven databases

    图  2  5个常用数据库功能注释维恩图

    Figure  2.  Venn diagram of Isoform annotations according to five databases

    图  3  NR数据库中比对到前10种物种名称及转录本数目

    Figure  3.  The top 10 species distribution annotated from NR database

    图  4  重瓣铁线莲全长转录本的GO功能注释

    Figure  4.  Gene Ontology classification of isoforms of Clematis florida

    图  5  重瓣铁线莲全长转录本的COG/KOG功能注释及分类

    Figure  5.  COG/KOG function annotation and classification of isoforms of Clematis florida

    图  6  重瓣铁线莲全长转录组SSR分布图

    Figure  6.  Distribution of SSR Motifs in of isoforms of Clematis florida

    图  7  SMRT 预测的前10个转录因子的数量和家族

    Figure  7.  Number and family of top 10 transcription factors predicted by SMRT

    图  8  重瓣铁线莲长非编码RNA分析结果

    Figure  8.  Result of long non-coding RNAs (lncRNAs) of Isoforms of Clematis florida

    图  9  重瓣铁线莲LncRNA与mRNA长度分布图

    Figure  9.  Distribution of length of LncRNA and mRNA in Clematis florida

    表  1  单分子实时测序数据统计

    Table  1.   Statistics of sequencing data by SMRT

    类别
    Type
    总数
    Total number
    最小长度
    Min length(bp)
    最大长度
    Max length(bp)
    平均长度
    Mean length(bp)
    N50长度
    N50 length(bp)
    原始序列中的单个子序列
    Subreads
    27863322 2233 2469
    环形一致性序列
    Circular consensus sequence (CCS)
    595827 54 14994 2488 2659
    全长非嵌序列
    Full-Length non-chimericRead (FLNC)
    494732 57 14860 2333 2531
    优化一致性序列
    Polished consensus sequence
    41768 87 6251 2272 2468
    去冗余高质量序列
    Isoform
    20540 87 6251 2248 2457
    下载: 导出CSV

    表  2  转录本KEGG注释结果

    Table  2.   KEGG annotation result of transcripts

    KEGG主通路
    Main pathway
    KEGG子通路
    Sub-pathway of KEGG
    转录本数量
    Number of
    transcripts
    KEGG主通路
    Main pathway
    KEGG子通路
    Sub-pathway of KEGG
    转录本数量
    Number of
    transcripts
    细胞过程
    Cellular Process
    运输与催化
    Transport and catabolism
    595代谢
    Metabolism
    异种生物降解和代谢
    Xenobiotics biodegradation and metabolism
    85
    细胞群落-原核生物
    Cellular community-prokaryotes
    93核酸代谢
    Nucleotide metabolism
    198
    细胞群落-真核生物
    Cellular community-eukaryotes
    124萜类和聚酮类代谢
    Metabolism of terpenoids and polyketides
    203
    细胞运动
    Cell motility
    39其他氨基酸代谢
    Metabolism of other amino acids
    333
    细胞生和与死亡
    Cell growth and death
    276辅助因子和维生素代谢
    Metabolism of cofactors and vitamins
    345
    环境信息处理
    Environmental
    information Processing
    信号转导
    Signal transduction
    984脂类代谢
    Lipid metabolism
    437
    膜运输
    Membrane transport
    51聚糖生物合成和代谢
    Glycan biosynthesis and metabolism
    171
    遗传信息处理
    Genetic information Processing
    翻译
    Translation
    806全局和总览图
    Global and overview maps
    718
    转录
    Trancription
    480能量代谢
    Eenergy metabolism
    540
    复制与修复
    replication and repair
    176碳水化合物代谢
    Carbohydrate metabolism
    1010
    折叠,分类和降解
    Folding, sorting and degradation
    657其他生长代谢物合成
    Biosynthesis of other secondary metabolites
    243
    人类疾病
    Human Diseases
    药物依赖
    Substance dependence
    44氨基酸代谢
    Amino acid metabolism
    561
    神经退行性疾病
    Neurodegenerative diseases
    165组织系统
    Organismal Systems
    感官系统
    Sensory system
    15
    感染疾病-病毒
    Infectious diseases:Viral
    496神经系统
    Nervours system
    294
    感染疾病-寄生生物
    Infectious diseases:Parasitic
    217免疫系统
    Immune system
    359
    感染疾病-细菌
    Infectious diseases:Bacterial
    309分泌系统
    Excretory system
    51
    免疫疾病
    Immune diseases
    35环境适应
    Environmental adaptation
    362
    内分泌与代谢疾病
    Endocrine and metabolic diseases
    141内分泌系统
    Endocrine system
    404
    耐药性:抗肿瘤药
    Drug resistance:Antineoplastic
    94消化系统
    Digestive system
    77
    心血管疾病
    Cardiovascular diseases
    88发育
    Development
    17
    癌症:特殊类型
    Cancers:Specific types
    86循环系统
    Circulatory system
    57
    癌症:总览
    Cancers:Overview
    384老龄化
    Aging
    148
    下载: 导出CSV

    表  3  重瓣铁线莲转录组中与萜类化合物合成相关的转录本

    Table  3.   The Isoforms encoding key enzymes involved in terpenoid biosynthesis in Clematis florida

    合成途径
    Pathway
    关键酶名称
    Key enzyme name
    酶的系统编号
    Enzyme No
    转录本数
    No. of Isoform
    MVA途径
    MVA Pathway
    羟甲基戊二酰辅酶A合酶
    hydroxymethylglutaryl-CoA synthase (HMGS)
    EC:2.3.3.10 1
    羟甲基戊二酰辅酶A还原酶
    hydroxymethylglutaryl-CoA reductase(HMGR)
    EC:1.1.1.34 2
    甲羟戊酸激酶
    mevalonate kinase(MK)
    EC:2.7.1.36 1
    磷酸甲羟戊酸激酶
    phosphomevalonate kinase(PMK)
    EC:2.7.4.2 1
    二磷酸甲羟戊酸脱羧酶
    diphosphomevalonate decarboxylase (MVD)
    EC:4.1.1.33 2
    MEP途径
    MEP Pathway
    1-脱氧-D-木酮糖5-磷酸合酶
    1-deoxy-D-xylulose-5-phosphate synthase(DXS)
    EC:2.2.1.7 11
    1-脱氧-D-木酮糖5-磷酸还原异构酶
    1-deoxy-D-xylulose-5-phosphate reductoisomerase(DXR)
    EC:1.1.1.267 5
    2-C-甲基-D-赤藓醇-4-磷酸胱氨酰转移酶
    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase(MCT)
    EC:2.7.7.60 1
    4-二磷酸二胺-2-C-甲基-D-赤藓糖醇激酶
    4-diphosphocytidyl-2-C-methyl-D-erythritol kinase(CMK)
    EC:2.7.1.148 1
    4-羟基-3-甲丁-2-烯基二磷酸合酶
    4-hydroxy-3-methylbut-2-enyl-diphosphate synthase(HDS)
    EC:1.17.7.1 9
    4-羟基-3-甲丁-2-烯基二磷酸还原酶
    4-hydroxy-3-methylbut-2-enyl diphosphate reductase(HDR)
    EC:1.17.7.4 2
    分支点
    Branch points
    异戊烯二磷酸Delta-异构酶
    Isopentenyl-diphosphate delta-isomerase(IPPI)
    EC:5.3.3.2 2
    牻牛儿基牻牛儿基焦磷酸合酶
    geranylgeranyl diphosphate synthase(GGPS)
    EC: 2.5.1.29 6
    法呢基焦磷酸合酶
    farnesyl diphosphate synthase(FPPS)
    EC:2.5.1.10 1
    蛋白香叶烯基转移酶 protein farnesyltransferase subunit (FNTB) EC:2.5.1.58 1
    内肽酶endopeptidase(STE24) EC:3.4.24.84 2
    下载: 导出CSV
  • [1] 黄泽豪, 张月玲. 畲药十二时辰的本草考证 [J]. 中国民族民间医药, 2014, 23(1):2−3,5.

    HUANG Z H, ZHANG Y L. Textual research on she medicine’s twelve o’clock materia Medica [J]. Chinese Journal of Ethnomedicine and Ethnopharmacy, 2014, 23(1): 2−3,5. (in Chinese)
    [2] 何舒澜, 杨谨, 黄娴, 等. 重瓣铁线莲鲨烯合酶SQS基因的克隆及表达分析 [J]. 福建农业学报, 2022, 37(11):1430−1437.

    HE S L, YANG J, HUANG X, et al. Cloning and expression of squalene synthase gene from Clematis florida Thunb. var. plena D. don [J]. Fujian Journal of Agricultural Sciences, 2022, 37(11): 1430−1437. (in Chinese)
    [3] 沈廷明, 黄春情, 吴军军, 等. GC-MS法分析畲药十二时辰花中挥发油成分 [J]. 中草药, 2020, 51(24):6362−6366.

    SHEN T M, HUANG C Q, WU J J, et al. GC-MS analysis of volatile oil from traditional She medicine Clematis florida var. plena flower [J]. Chinese Traditional and Herbal Drugs, 2020, 51(24): 6362−6366. (in Chinese)
    [4] YANG N N, ZHANG Y F, ZHANG H T, et al. The in vitro and in vivo anti-inflammatory activities of triterpene saponins from Clematis florida [J]. Natural Product Research, 2021, 35(24): 6180−6183. doi: 10.1080/14786419.2020.1833203
    [5] SUN K H, MA X H, ZENG X M, et al. A new indole-type alkaloid from the roots of Clematis florida var. plena [J]. Natural Product Research, 2019, 33(20): 2925−2931. doi: 10.1080/14786419.2018.1510396
    [6] WU Y, ZHANG Y F, ZHANG H T, et al. A new cyclopeptide alkaloid from Clematis Florida [J]. Natural Product Research, 2022, 36(7): 1693−1699. doi: 10.1080/14786419.2020.1809399
    [7] 黄丽容, 郭晓云, 胡营, 等. 香附子全长转录组测序及生物信息学分析 [J]. 中国现代中药, 2023, 25(7):1428−1440.

    HUANG L R, GUO X Y, HU Y, et al. Full-length transcriptome sequencing and bioinformatics analysis of Cyperus rotundus L [J]. Modern Chinese Medicine, 2023, 25(7): 1428−1440. (in Chinese)
    [8] 米琪, 赵艳丽, 徐萍, 等. 滇黄精全长转录组测序及生物信息学分析 [J]. 药学学报, 2024, 59(6):1864−1872.

    MI Q, ZHAO Y L, XU P, et al. Full-length transcriptome sequencing and bioinformatics analysis of Polygonatum kingianum [J]. Acta Pharmaceutica Sinica, 2024, 59(6): 1864−1872. (in Chinese)
    [9] HE B, SHAN T Y, XU J Y, et al. Full-length transcriptome profiling of Acanthopanax gracilistylus provides new insight into the kaurenoic acid biosynthesis pathway [J]. Physiology and Molecular Biology of Plants, 2024, 30(3): 383−399. doi: 10.1007/s12298-024-01436-7
    [10] BUCHFINK B, XIE C, HUSON D H. Fast and sensitive protein alignment using DIAMOND [J]. Nature Methods, 2015, 12(1): 59−60. doi: 10.1038/nmeth.3176
    [11] ZHENG Y, JIAO C, SUN H H, et al. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases [J]. Molecular Plant, 2016, 9(12): 1667−1670. doi: 10.1016/j.molp.2016.09.014
    [12] THIEL T, MICHALEK W, VARSHNEY R K, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L. ) [J]. TAG Theoretical and Applied Genetics Theoretische und Angewandte Genetik, 2003, 106(3): 411−422. doi: 10.1007/s00122-002-1031-0
    [13] SUN L, LUO H T, BU D C, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts [J]. Nucleic Acids Research, 2013, 41(17): e166. doi: 10.1093/nar/gkt646
    [14] KANG Y J, YANG D C, KONG L, et al. CPC2: A fast and accurate coding potential calculator based on sequence intrinsic features [J]. Nucleic Acids Research, 2017, 45(W1): W12−W16. doi: 10.1093/nar/gkx428
    [15] FINN R D, COGGILL P, EBERHARDT R Y, et al. The pfam protein families database: Towards a more sustainable future [J]. Nucleic Acids Research, 2016, 44(D1): D279−D285. doi: 10.1093/nar/gkv1344
    [16] LI A M, ZHANG J Y, ZHOU Z Y. PLEK: A tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme [J]. BMC Bioinformatics, 2014, 15(1): 311. doi: 10.1186/1471-2105-15-311
    [17] 沈廷明, 陈懿冲, 黄春情, 等. 畲药十二时辰的质量标准研究 [J]. 海峡药学, 2023, 35(8):36−41.

    SHEN T M, CHEN Y C, HUANG C Q, et al. Quality standard of she medicine Clematis florida var. plena [J]. Strait Pharmaceutical Journal, 2023, 35(8): 36−41. (in Chinese)
    [18] 陈懿冲, 沈廷明, 陈艳柠, 等. 基于网络药理学探讨畲药十二时辰镇痛作用机制 [J]. 海峡药学, 2024, 36(1):1−6.

    CHEN Y C, SHEN T M, CHEN Y N, et al. Based on the network pharmacology to explore the mechanism of analgesic action of she medicine Clematis florida var. flore-pleno [J]. Strait Pharmaceutical Journal, 2024, 36(1): 1−6. (in Chinese)
    [19] JIANG C H, BI Y K, MO J B, et al. Proteome and transcriptome reveal the involvement of heat shock proteins and antioxidant system in thermotolerance of Clematis florida [J]. Scientific Reports, 2020, 10(1): 8883. doi: 10.1038/s41598-020-65699-2
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出版历程
  • 收稿日期:  2024-08-02
  • 录用日期:  2024-10-16
  • 修回日期:  2024-09-12
  • 网络出版日期:  2024-11-11

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