Regulation mechanism of long non-coding RNA in plant secondary metabolite biosynthesis


  • Yuting LI Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)
  • Huan HAN Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)
  • Jiabao YE Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)
  • Feng XU Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)
  • Weiwei ZHANG Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)
  • Yongling LIAO Yangtze University, College of Horticulture and Gardening, Jingzhou 434025, Hubei (CN)



alkaloid, flavonoids, lncRNA, secondary metabolites, terpenoids


Long non-coding RNAs (lncRNAs) are widely available transcription products of more than 200 nucleotides with unrecognizable coding potential. A large number of lncRNAs have been identified in different plants. lncRNAs are involved in various basic biological processes at the transcriptional, post-transcriptional and epigenetic levels as key regulatory molecules, including in the regulation of flowering time and reproductive organ morphogenesis, and they play important roles in the biosynthesis of plant secondary metabolites. In this paper, we review the research strategies of lncRNAs and lncRNAs related to the biosynthesis of plant secondary metabolites, focusing on the research strategies for studying lncRNAs and the effects of lncRNAs on the biosynthesis of terpenoids, alkaloids and flavonoids, aiming to provide new ideas for the study of the regulation of plant secondary metabolite biosynthesis.


Andersen ØM, Jordheim M (2010). Chemistry of flavonoid-based colors in plants. In: Comprehensive Natural Products II. Elsevier, Oxford, pp 547-614.

Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M (2015). Battles and hijacks: noncoding transcription in plants. Trends in Plant Science 20:362-371.

Armaos A, Colantoni A, Proietti G, Rupert J, Tartaglia GG (2021). catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions. Nucleic Acids Research 49:W72-W79.

Baulcombe DC (1999). Fast forward genetics based on virus-induced gene silencing. Current Opinion in Plant Biology 2:109-113.

Becker A, Lange M (2010). VIGS – genomics goes functional. Trends in Plant Science 15:1-4.

Carlevaro-Fita J, Johnson R (2019). Global positioning system: understanding long noncoding RNAs through subcellular localization. Molecular Cell 73:869-883.

Chen J, Tang X, Ren C, Wei B, Wu Y, Wu Q, Pei J (2018). Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. BMC Genomics 19:548.

Chen L (2016). Linking long noncoding RNA localization and function. Trends in Biochemical Sciences 41,761-772.

Chen X, Sun S, Liu F, Shen E, Liu L (2019). A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). BMC Genomics 20:856.

Chen Y, Cheng C, Feng X, Lai R, Gao M, Chen W, Wu RJ (2021). Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening. Scientific Reports 11:1671.

Ci D, Tian M, Song Y, Du Q, Quan M (2019). Indole-3-acetic acid has long-term effects on long non-coding RNA gene methylation and growth in Populus tomentosa. Molecular Genetics and Genomics 294:1511-1525.

Crespi MD, Jurkevitch E, Poiret M, d’Aubenton-Carafa Y, Petrovics G, Kondorosi E, Kondorosi A (1994). enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. The EMBO Journal 13:5099-5112.

Cui C, Shu W, Li P (2016). Fluorescence in situ hybridization: cell-based genetic diagnostic and research applications. Frontiers in Cell and Developmental Biology 4:89.

Cui J, Shen N, Lu Z, Xu G, Wang Y, Jin B (2020). Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome. Plant Methods 16:85.

Cui J, Jiang N, Meng J, Yang G, Liu W, Zhou X, … Luan Y (2019). LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions. The Plant Journal: For Cell and Molecular Biology 97(5):933-946.

Dalmay T (2013). Mechanism of miRNA-mediated repression of mRNA translation. Essays in Biochemistry 54:29-38.

Dewey RE, Xie J (2013). Molecular genetics of alkaloid biosynthesis in Nicotiana tabacum. Phytochemistry 94:10-27.

Fang J, Zhang F, Wang H, Wang W, Zhao F, Li Z, … Chu C (2019). Ef-cd locus shortens rice maturity duration without yield penalty. Proceedings of the National Academy of Sciences of the United States of America 116(37):18717-18722.

Fok ET, Scholefield J, Fanucchi S, Mhlanga MM (2017). The emerging molecular biology toolbox for the study of long noncoding RNA biology. Epigenomics 9(10):1317-1327.

Fukuda M, Nishida S, Kakei Y, Shimada Y, Fujiwara T (2019). Genome-wide analysis of long intergenic noncoding RNAs responding to low-nutrient conditions in Arabidopsis thaliana: possible involvement of trans-acting siRNA3 in response to low nitrogen. Plant and Cell Physiology 60(9):1961-1973.

Gai Y, Yuan S, Zhao Y, Zhao H, Zhang H, Ji X (2018). A novel lncRNA, MuLnc1, associated with environmental stress in Mulberry (Morus multicaulis). Frontiers in Plant Science 9:669.

Gao R, Liu P, Irwanto N, Loh DR, Wong S (2016). Upregulation of LINC-AP2 is negatively correlated with AP2 gene expression with Turnip crinkle virus infection in Arabidopsis thaliana. Plant Cell Reports 35(11):2257-2267.

Guo G, Liu X, Sun F, Cao J, Huo N, Wuda B, … Yao Y (2018). Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acid/gibberellin signaling. The Plant Cell 30(4):796-814.

Hartmann T (2007). From waste products to ecochemicals: fifty years research of plant secondary metabolism. Phytochemistry 68(22-24):2831-2846.

Hou X, Cui J, Liu W, Jiang N, Zhou X, Qi H, … Luan Y (2020). LncRNA39026 enhances tomato resistance to Phytophthora infestans by decoying miR168a and inducing PR gene expression. Phytopathology 110(4):873-880.

Hussain B, Lucas SJ, Budak H (2018). CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement. Briefings in Functional Genomics 17(5):319-328.

Jain N, Sinha N, Krishna H, Singh PK, Gautam T, Prasad P, … Gupta PK (2020). A study of miRNAs and lncRNAs during Lr28-mediated resistance against leaf rust in wheat (Triticum aestivum L.) Physiological and Molecular Plant Pathology 112:101552.

Jiang N, Cui J, Shi Y, Yang G, Zhou X, Hou X, … Luan Y (2019). Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction. Horticulture Research 6:28.

Jiang N, Cui J, Hou X, Yang G, Xiao Y, Han L, … Luan Y (2020). Sl-lncRNA15492 interacts with Sl-miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans. The Plant Journal: For Cell and Molecular Biology 103(4):1561-1574.

Karlova R, van Haarst JC, Maliepaard C, van de Geest H, Bovy AG, Lammers M, … de Maagd RA (2013). Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. Journal of Experimental Botany 64(7):1863-1878.

Kim D-H, Sung S (2017). Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Developmental Cell 40(3):302-312.

Kim D-H, Xi Y, Sung S (2017). Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genetics 13(7):e1006939.

Kutchan TM (2001). Ecological arsenal and developmental dispatcher. The paradigm of secondary metabolism. Plant Physiology 125(1):58-60.

Lennox KA, Behlke MA (2016). Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Research 44(2):863-877.

Li F, Wang W, Zhao N, Xiao B, Cao P, Wu X, … Fan L (2015). Regulation of nicotine biosynthesis by an endogenous target mimicry of microRNA in tobacco. Plant Physiology 169(2):1062-1071.

Li H, Ye W, Wang Y, Chen X, Fang Y, Sun G (2021). RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response of D. officinale. PeerJ 9:e10769.

Li J, Ma W, Zeng P, Wang J, Geng B, Yang J, Cui Q (2015). LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Briefings in Bioinformatics 16(5):806-812.

Li J, Wu B, Xu J, Liu C (2014). Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum. PLOS ONE 9(6):e99442.

Li R, Fu D, Zhu B, Luo Y, Zhu H (2018). CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. The Plant Journal: For Cell and Molecular Biology 94(3):513-524.

Li Y, Qin T, Dong N, Wei C, Zhang Y, Sun R, … Wang Q (2019). Integrative analysis of the lncRNA and mRNA transcriptome revealed genes and pathways potentially involved in the anther abortion of Cotton (Gossypium hirsutum L.). Genes 10(12):E947.

Liao X, Wang J, Zhu S, Xie Q, Wang L, Yu H, … Yang C (2020). Transcriptomic and functional analyses uncover the regulatory role of lncRNA000170 in tomato multicellular trichome formation. The Plant Journal: For Cell and Molecular Biology 104(1):18-29.

Lin Y, Jiang L, Chen Q, Li Y, Zhnag Y, Sun B, … Tang Haoru (2018). Comparative transcriptome profiling analysis of red- and white-fleshed Strawberry (Fragaria×ananassa) provides new insight into the regulation of the anthocyanin pathway. Plant & Cell Physiology 59(9):1844-1859.

Liu S, Wang Lu, Cao M, Pang S, Li W, Kato-Noguchi H, … Wang L (2020). Identification and characterization of long non-coding RNAs regulating flavonoid biosynthesis in Ginkgo biloba leaves. Industrial Crops and Products 158:112980.

Lu Q, Ren S, Lu M, Zhang Y, Zhu D, Zhnag X, Li T (2013). Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics 14:651.

Ma H, Yang T, Li Y, Zhang J, Wu T, Song T, … Tian J (2021). The long noncoding RNA MdLNC499 bridges MdWRKY1 and MdERF109 function to regulate early-stage light-induced anthocyanin accumulation in apple fruit. The Plant Cell 188.

Ma L, Bajic VB, Zhang Z (2013). On the classification of long non-coding RNAs. RNA Biology 10(6):924-933.

Narnoliya LK, Kaushal G, Singh SP (2019). Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium. FEBS letters 593(16):2235-2249.

Nejat N, Mantri N (2018). Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses. Critical Reviews in Biotechnology 38(1):93-105.

Ni Z, Han X, Chen C, Zhong Y, Xu M, Xu L, Yu F (2021). Integrating GC-MS and ssRNA-Seq analysis to identify long non-coding RNAs related to terpenoid biosynthesis in Cinnamomum camphora. Industrial Crops and Products 171:113875.

Pachnis V, Belayew A, Tilghman SM (1984). Locus unlinked to alpha-fetoprotein under the control of the murine raf and Rif genes. Proceedings of the National Academy of Sciences of the United States of America 81(17):5523-5527.

Ponjavic J, Ponting CP, Lunter G (2007). Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Research 17(5):556-565.

Ponting CP, Oliver PL, Reik W (2009). Evolution and functions of long noncoding RNAs. Cell 136(4):629-641.

Qiao D, Yang C, Chen J, Guo Y, Li Y, Niu S, … Chen Z (2019). Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis). Scientific Reports 9(1):2709.

Qin T, Zhao H, Cui P, Albesher N, Xiong L (2017). A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiology 175(3):1321-1336.

Quan M, Xiao L, Lu W, Liu X, Song F, Si J, … Zhang D (2018). Association genetics in Populus reveal the allelic interactions of Pto-MIR167a and its targets in wood formation. Frontiers in Plant Science 9:744.

Roberts RJ, Carneiro MO, Schatz MC (2013). The advantages of SMRT sequencing. Genome Biology 14(6):405.

Saitoh F, Noma M, Kawashima N (1985). The alkaloid contents of sixty Nicotiana species, Phytochemistry, 24(3):477-480.

Seo JS, Sun HX, Park BS, Huang CH, Yeh S, Jung C, Chua NH (2017). ELF18-INDUCED LONG-NONCODING RNA associates with mediator to enhance expression of innate immune response genes in Arabidopsis. The Plant Cell 29(5):1024-1038.

Seo JS, Chua N-H (2019a). Identification of long noncoding RNA-protein interactions through in vitro RNA pull-down assay with plant nuclear extracts. Methods in Molecular Biology (Clifton, N.J.) 1933:279-288.

Seo JS, Chua N-H (2019b). Trimolecular fluorescence complementation (TriFC) assay for visualization of RNA-protein interaction in plants. Methods in Molecular Biology (Clifton, N.J.) 1933:297-303.

Song L, Fang Y, Chen L, Wang J, Chen X (2021). Role of non-coding RNAs in plant immunity. Plant Communications 2(3):100180.

Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr A, … Odom DT (2018). Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Nucleic Acids Research 46(12):5950-5966.

Takshak S, Agrawal SB (2019). Defense potential of secondary metabolites in medicinal plants under UV-B stress. Journal of Photochemistry and Photobiology, B: Biology 193:51-88.

Wang J, Meng X, Dobrovolskaya OB, Orlov YL, Chen M (2017). Non-coding RNAs and their roles in stress response in plants, Genomics. Proteomics & Bioinformatics 15(5):301-312.

Wink M (2015). Modes of action of herbal medicines and plant secondary metabolites. Medicines (Basel, Switzerland) 2(3):251-286.

Wu B, Li Y, Yan H, Ma Y, Luo H, Yuan L, … Lu S (2012). Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics 13:15.

Wu H, Wang Z, Wang M, Wang X (2013). Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiology 161(4):1875-1884.

Xiao Y, Kang B, Li M, Xiao L, Xiao H, Shen H, Yang W (2020). Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato. RNA Biology 17(4):596-607.

Xie J, Fan L (2016). Nicotine biosynthesis is regulated by two more layers: Small and long non-protein-coding RNAs. Plant Signaling & Behavior 11(6):e1184811.

Xin M, Wang Y, Yao Y, Song N, Hu Z, Qin D, … Sun Q (2011). Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biology 11:61.

Yang T, Ma H, Zhang J, Wu T, Song T, Tian J, Yao Y (2019). Systematic identification of long noncoding RNAs expressed during light-induced anthocyanin accumulation in apple fruit. The Plant Journal: For Cell and Molecular Biology 100(3):572-590.

Ye J, Cheng S, Zhou X, Chen Z, Kin SU, Tan J, … Zhu Y (2019). A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis. Industrial Crops and Products 139:111547.

Yu J, Qiu K, Sun W, Yang T, Wu T, Song T, … Tian J (2022). A long noncoding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis. Plant Physiology kiac049.

Zhang G, Duan A, Zhang J, He C (2017). Genome-wide analysis of long non-coding RNAs at the mature stage of sea buckthorn (Hippophae rhamnoides Linn) fruit. Gene 596:130-136.

Zhang G, Chen D, Zhang T, Duan A, Zhang J, He C (2018). Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening. DNA Research 25(5):465-476.

Zhang G, Sun M, Wang J, Lei M, Li C, Zhao D, … Zhang B (2019). PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice. The Plant Journal 97(2):296-305.

Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, … Wu Y (2021). Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Molecular Cancer 20(1):126.

Zhang X, Dong J, Deng F, Wang W, Cheng Y, Song L, … Shen F (2019). The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. BMC Plant Biology 19(1):459.

Zhang X, Shen J, Xu Q, Dong J, Song L, Wang W, Shen F (2021). Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton. Plant, Cell & Environment 44(10):3302-3321.

Zhao X, Li J, Lian B, Gu H, Li Y, Qi Y (2018). Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nature Communications 9(1):5056.

Zhou M, Zhu X, Shao J, Tang Y, Wu Y (2011). Production and metabolic engineering of bioactive substances in plant hairy root culture. Applied Microbiology and Biotechnology 90(4):1229-1239.

Zhou W, Shi H, Wang Z, Zhao Y, Gou X, Li C, … Liu Y (2020). Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines. Functional & Integrative Genomics 20(5):669-679.

Zou C, Wang Q, Lu C, Yang W, Zhang Y, Cheng H, … Song G (2016). Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum). Science China. Life Sciences 59(2):164-171.



How to Cite

LI, Y., HAN, H., YE, J., XU, F., ZHANG, W., & LIAO, Y. (2022). Regulation mechanism of long non-coding RNA in plant secondary metabolite biosynthesis. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(2), 12604.



Review Articles
DOI: 10.15835/nbha50212604

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