Tanmay Ghosh and Rishin Bhattacharyya

¹Department of Microbiology, Dinabandhu Andrews College, Baishnabghata, South 24 Parganas, Kolkata 700084, West Bengal, India
²Department of Botany, Brahmananda Keshab Chandra College, Baranagar-700108, West Bengal, India

*Corresponding Author: Tanmay Ghosh, Department of Microbiology, Dinabandhu Andrews College, Baishnabghata, South 24 Parganas, Kolkata 700084, West Bengal, India.

Received: January 19, 2026; Published: January 31, 2026

Abstract

Plant secondary metabolites have important effects on medicine, agriculture, and ecological relationships. They are essential for many biological processes. As RNAi technology has advanced, it has made it possible to study gene regulation and control the production of secondary metabolites in plants. Here we aimed to examine the function of RNAi technology in controlling secondary metabolite biosynthesis in plants. In this review, the use of RNAi technology in riboregulating secondary metabolites and its manipulation in plants were studied. The experimental strategies used to understand the role of RNAi technology on natural product levels and the variety of RNAi techniques utilized for these tasks along with pinpointing any potential future uses were investigated to decipher the intricacies of plant secondary metabolite pathways and methods of post transcriptional gene silencing by various types of non coding RNAs. This study also reviewed the evolution of RNAi technology over time, tracking its beginnings to its application in plant systems. These findings could be successfully applied to regulate secondary metabolite biosynthesis in plants which illustrated the capability of RNAi in regulating the synthesis of useful secondary metabolites for various applications. A thorough and comprehensive literature review through various biological databases like PubMed, Springer Nature, ResearchGate, Google Scholar, Web of Science, ScienceDirect etc. was done for this work. We used keywords such as PTGS (Post Transcriptional Gene Silencing), RNAi (RNA interference), riboregulation, secondary metabolite biosynthesis etc. The future potential of RNAi in controlling the secondary metabolites in plants was discussed in the current review. This work also explored how machine learning algorithms might improve target identification, delivery effectiveness, and precision in RNAi-based techniques by incorporating artificial intelligence (AI) driven strategies. It highlighted the promise of RNAi as a game-changing tool in plant research to envision a bright future which will change secondary metabolite management for numerous practical applications.

Keywords: Plant Secondary Metabolites; RNA Interference (RNAi) Technology; Secondary Metabolite Biosynthesis; Riboregulation; Experimental Strategies; Post-Transcriptional Gene Silencing; Non-coding RNAs

References

1. Hasler CM and Blumberg JB. “Phytochemicals: biochemistry and physiology”. Journal of Nutrition 129 (1999): 756S-757S.
2. Gibson EL., et al. “Fruit and vegetable consumption, nutritional knowledge and beliefs in mothers and children”. Appetite 31 (1998): 205-228.
3. Mathai K. “Nutrition in the adult years”. In: Kathleen ML, Sylvia E-S (eds) Krause’s food, nutrition, and diet therapy, vol 271. Saunders, Philadelphia (2000): 274-275.
4. Harborne JB and Baxter H. “Phytochemical dictionary”. A handbook of bioactive compounds from plants”. Taylor & Francis Limited, Milton Park.
5. Saxena M., et al. “Phytochemistry of medicinal plants”. Journal of Pharmacognosy and Phytochemistry6 (2013).
6. Samrot AV., et al. “Evaluation of bioactivity of various Indian medicinal plants—an in-vitro study”. Journal of Internal Medicine2 (2009).
7. Dai J., et al. “Plant phenolics: extraction, analysis and their antioxidant and anticancer properties”. Molecules 15 (2010): 7313-7352.
8. Costa MA., et al. “Toward engineering the metabolic pathways of cancer-preventing lignans in cereal grains and other crops”. In: Romeo JT (ed) Phytochemicals in human health protection, nutrition, and plant defense. Springer, Boston, MA, (1999): 67-87.
9. Rao BN. “Bioactive phytochemicals in Indian foods and their potential in health promotion and disease prevention”. Asia Pacific Journal of Clinical Nutrition1 (2003): 9-22.
10. Hamburger M and Hostettmann K. “Bioactivity in plants: the link between phytochemistry and medicine”. Phytochemistry 30 (1991): 3864-3874.
11. Ncube NS., et al. “Assessment techniques of antimicrobial properties of natural compounds of plant origin: current methods and future trends”. African Journal of Biotechnology 7 (2008): 1797-1806.
12. Liu RH. “Health-promoting components of fruits and vegetables in the diet”. Advances in Nutrition 4 (2013): 384S-392S.
13. Hahn NI. “Are phytoestrogens nature’s cure for what ails us? A look at the research”. Journal of the American Dietetic Association 98 (1998): 974-977.
14. Ramawat KG., et al. “The chemical diversity of bioactive molecules and therapeutic potential of medicinal plants”. In: Ramawat KG (ed) Herbal drugs: ethnomedicine to modern medicine. Springer Nature, Switzerland (2009): 7-32.
15. Pullela R., et al. “A case of fatal aconitine poisoning by Monkshood ingestion”. Journal of Forensic Science 53 (2008): 491-494.
16. Dimitrov K., et al. “Integrated processes of extraction and liquid membrane isolation of atropine from Atropa belladonna roots”. Separation and Purification Technology 46 (2005): 41-45.
17. Perrois C., et al. “Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta)”. Planta 241 (2015): 179-191.
18. Gasparyan AY., et al. “Colchicine as an anti-inflammatory and cardioprotective agent”. Expert Opinion on Drug Metabolism and Toxicology 11 (2015): 1781-1794.
19. Fischman MW and Foltin RW. “Cocaine and the amphetamines”. In: Glass IB (ed) The international handbook of addiction behavior, vol 11. Routledge, Milton Park, UK (2021): 85-89.
20. Mani D and Dhawan SS. “Scientific basis of therapeutic uses of Opium poppy (Papaver somniferum) in Ayurveda”. In International symposium on papaver (2011): 175-180.
21. Bhuju S and Gauchan DP. “Taxus wallichiana (Zucc.), an endangered anti-cancerous plant: a review”. International Journal of Research 5 (2018): 10-21.
22. Imenshahidi M., et al. “Berberis vulgaris and berberine: an update review”. Phytotherapy Research 30 (2016): 1745-1764.
23. Jing Y., et al. “Electrodeposition of Au nanoparticles on poly (diallyldimethylammonium chloride) functionalized reduced graphene oxide sheets for voltammetric determination of nicotine in tobacco products and anti-smoking pharmaceuticals”. RSC Advances 2016 (2016): 26247-26253.
24. Smakosz A., et al. “The usage of ergot (Claviceps purpurea (fr.) Tul.) in obstetrics and gynecology: a historical perspective”. Toxins 13 (2021): 492.
25. Gutzeit HO and Ludwig MJ. “Plant natural products: synthesis, biological functions and practical applications”. Wiley, Hoboken, NJ (2014): 40.
26. Rodriguez-Garcia A., et al. “Multi-target activities of selected alkaloids and terpenoids”. Mini-Reviews in Organic Chemistry 14 (2017): 272-279.
27. Fresco P., et al. “New insights on the anticancer properties of dietary polyphenols”. Medicinal Research Reviews 26 (2006): 747-766.
28. Cheynier V., et al. “Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology”. Plant Physiology and Biochemistry 72 (2013): 1-20.
29. Liew ST and Yang LX. “Design, synthesis and development of novel camptothecin drugs”. Current Pharmaceutical Design 11 (2008): 1078-1097.
30. Dubey VS., et al. “An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants”. Journal of Bioscience 28 (2003): 637-646.
31. Ekor M. “The growing use of herbal medicines: issues relating to adverse reactions and challenges in monitoring safety”. Frontiers in Pharmacology 4 (2014): 177.
32. Caplen NJ., et al. “dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference”. Gene1-2 (2000): 95-105.
33. Fire AZ and Mello CC. “The nobel prize in physiology or medicine 2006”. Nobel Media AB (2014).
34. Grishok A., et al. “Genetic requirements for inheritance of RNAi in C. elegans”. Science5462 (2000): 2494-2497
35. Borgio JF. “RNA interference (RNAi) technology: a promising tool for medicinal plant research”. Journal of Medical Plant Research 13 (2009): 1176-1183.
36. Hammond SM., et al. “An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells”. Nature 6775 (2000): 293-296.
37. Bernstein E., et al. “Role for a bidentate ribonuclease in the initiation step of RNA interference”. Nature 6818 (2001): 363-366.
38. Jaronczyk K., et al. “Exploring the functions of RNA interference pathway proteins: some functions are more RISCy than others?” Biochemistry Journal 3 (2005): 561-571.
39. Venkataraman S., et al. “RNA dependent RNA polymerases: insights from structure, function and evolution”. Viruses2 (2018): 76.
40. Fire A., et al. “Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans”. Nature 6669 (1998): 806-811.
41. Sijen T., et al. “On the role of RNA amplification in dsRNA-triggered gene silencing”. Cell4 (2001): 465-476.
42. Escobar MA., et al. “Post-transcriptional gene silencing in plants”. In: Barciszewski J (ed) Noncoding RNAs: molecular biology and molecular medicine. Kluwer Academic, Dordrecht, pp 129-140.
43. Waterhouse PM., et al. “Gene silencing as an adaptive defence against viruses”. Nature6839 (2001): 834-842.
44. Hannon GJ. “RNA interference”. Nature6894 (2002): 244-251.
45. Aukerman MJ and Sakai H. “Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes”. Plant Cell 11 (2003): 2730-2741.
46. Kusaba M. “RNA interference in crop plants”. Current Opinion on Biotechnology2 (2004): 139-143.
47. Fan R., et al. “Differential microRNA analysis of glandular trichomes and young leaves in Xanthium strumarium L. reveals their putative roles in regulating terpenoid biosynthesis”. PLoS One9 (2015): e0139002.
48. Zhang G., et al. “Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening”. DNA Research 25 (2018): 465-476.
49. Zhu C., et al. “Transcriptome and phytochemical analyses provide new insights into long non-coding RNAs modulating characteristic secondary metabolites of oolong tea (Camellia sinensis) in solar-withering”. Frontiers in Plant Science 10 (2019): 1638.
50. Vashisht I., et al. “Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa”. Planta 241 (2015): 1255-1268.
51. Yu Z-X., et al. “Progressive regulation of sesquiterpene biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-targeted SPL transcription factors”. Molecular Plant 8 (2015): 98-110.
52. Ye J., et al. “Global identification of Ginkgo biloba microRNAs and insight into their role in metabolism regulatory network of terpene trilactones by high-throughput sequencing and degradome analysis”. Indian Crop Production 148 (2020): 112289.
53. Sobhani Najafabadi A., et al. “Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes”. Gene 645 (2018): 41-47.
54. Narnoliya LK., et al. “Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium”. FEBS Letter 593 (2019): 2235-2249.
55. Singh N and Sharma A. “Turmeric (Curcuma longa): miRNAs and their regulating targets are involved in development and secondary metabolite pathways”. C R Biology x340 (2017): 481-491.
56. Deng K., et al. “Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway”. PeerJournal 9 (2021): e10704.
57. Khan S., et al. “Identification and the potential involvement of miRNAs in the regulation of artemisinin biosynthesis in A. annua”. Scientific Report 10 (2020): 13614.
58. Srivastava S., et al. “Comparative Study of Withanolide Biosynthesis-Related miRNAs in Root and Leaf Tissues of Withania somnifera”. Applied Biochemistry and Biotechnology4 (2018): 1145-1159.
59. Jannesar M., et al. “A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing”. Scientific Report 10 (2020).
60. Chun HJ., et al. “Lignin biosynthesis genes play critical roles in the adaptation of Arabidopsis plants to high-salt stress”. Plant Signaling and Behavior 14 (2019): 1625697.
61. He H., et al. “Two young microRNAs originating from target duplication mediate nitrogen starvation adaptation via regulation of glucosinolate synthesis in Arabidopsis thaliana”. Plant Physiology 164 (2013): 853-865.
62. Liang G., et al. “Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana”. PLoS One 7 (2011): e48951.
63. Mao Y-B., et al. “Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance.” Nature Communication 8 (2017): 13925.
64. Li F., et al. “Regulation of nicotine biosynthesis by an endogenous target mimicry of microRNA in tobacco”. Plant Physiology 169 (2015): 1062-1071.
65. Boke H., et al. “Regulation of the alkaloid biosynthesis by miRNA in opium poppy”. Plant Biotechnology 13 (2015): 409-420.
66. Tuteja JH., et al. “Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats”. Plant Cell 21 (2009): 3063-3077.
67. Luo Y., et al. “Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing”. BMC Plant Biology 15 (2015): 11.
68. Chen L., et al. “Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress”. BMC Genomics 19 (2018): 460.
69. Biswas S., et al. “Identification of conserved miRNAs and their putative target genes in Podophyllum hexandrum (Himalayan Mayapple)”. Plant Gene 6 (2016): 82-89.
70. Liu J., et al. “Regulation of fatty acid and flavonoid biosynthesis by miRNAs in Lonicera japonica”. RSC Advances 7 (2017): 35426-35437.
71. Li H., et al. “Relationship between secondary metabolism and miRNA for important flavor compounds in different tissues of tea plant (Camellia sinensis) as revealed by genome-wide miRNA analysis”. Journal of Agricultural and Food Chemistry6 (2021).
72. Shi Y., et al. “Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans”. BMC Genomics 22 (2021): 141.
73. Gou J-Y., et al. “Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor”. Plant Cell 23 (2011): 1512-1522.
74. Barozai MYK., et al. “Identification of MicroRNAs and their targets in Helianthus”. Molecular Biology Reports 39 (2012): 2523-2532.
75. Sharma R., et al. “RNAi mediated silencing of gene encoding 1-deoxy-D-Xylulose-5-phosphate reductoisomerase (DXR) in Centella asiatica”. American Journal of Plant Sciences11 (2020): 1723-1738.
76. Kalita R., et al. “RNAi mediated silencing of 3-hydroxy-3-methylglutaryl-CoA reductases (HMGR) in Centella asiatica”. Gene Report 11 (2018): 52-57.
77. Kumar R., et al. “RNAi down-regulation of cinnamate-4-hydroxylase increases artemisinin biosynthesis in Artemisia annua”. Scientific Report 6 (1 (2016): 1-2.
78. Wang CH., et al. “Effect of down-regulating 1-deoxy-D-xylulose-5- phosphate reductoisomerase by RNAi on growth and artemisinin biosynthesis in Artemisia annua L”. Plant Growth Regulation3 (2018): 549-559.
79. Fu X., et al. “AaPDR3, a PDR transporter 3, is involved in sesquiterpene β-caryophyllene transport in Artemisia annua”. Frontiers in Plant Science 8 (2017): 723.
80. Ali A., et al. “RNAi-mediated modulation of squalene synthase gene expression in Artemisia annua L. and its impact on artemisinin biosynthesis”. Rendicontion Lincei4 (2017): 731-741.
81. Hao X., et al. “Light-induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annua”. Plant Cell Physiology8 (2019): 1747-1760.
82. Yang Y., et al. “Strengthening triterpene saponins biosynthesis by over-expression of farnesyl pyrophosphate synthase gene and RNA interference of cycloartenol synthase gene in Panax notoginseng cells”. Molecules4 (2017): 581
83. Yang Y., et al. “RgC3H involves in the biosynthesis of allelopathic phenolic acids and alters their release amount in Rehmannia glutinosa roots”. Plan Theory5 (2020): 567.
84. Xiao Y., et al. “IiWRKY34 positively regulates yield, lignan biosynthesis and stress tolerance in Isatis indigotica”. Acta Pharm Sin B12 (2020): 2417-2432.
85. Jiang J., et al. “MYB43 in oilseed rape (Brassica napus) positively regulates vascular lignification, plant morphology and yield potential but negatively affects resistance to Sclerotinia sclerotiorum”. Genes 5 (2020): 581.
86. Wu Z., et al. “Simultaneous regulation of F5H in COMT-RNA i transgenic switchgrass alters effects of COMT suppression on syringyl lignin biosynthesis”. Plant Biotechnology4 (2019): 836-845.
87. Allen RS., et al. “RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy”. Nature Biotechnology12 (2004): 1559-1566.
88. Gourlay G., et al. “MYB134-RNAi poplar plants show reduced tannin synthesis in leaves but not roots, and increased susceptibility to oxidative stress”. Journal of Experimental Botany20 (2020): 6601-6611
89. Fan G., et al. “GSNOR deficiency enhances betulin production in Betula platyphylla”. Trees3 (2018): 847-853.
90. Yin J., et al. “Expression characteristics and function of CAS and a new beta-amyrin synthase in triterpenoid synthesis in birch (Betula platyphylla Suk.)”. Plant Science 294 (2020): 110433.
91. Martinez DH., et al. “Genetic attenuation of alkaloids and nicotine content in tobacco (Nicotiana tabacum)”. Planta 4 (2020): 1-14.
92. Wang Z., et al. “Functional characterization of a HD-ZIP IV transcription factor NtHDG2 in regulating flavonols biosynthesis in Nicotiana tabacum”. Plant Physiology and Biochemistry 146 (2020): 259-268.
93. Mitra S., et al. “Deciphering the Potential of RNAi Technology as Modulator of Plant Secondary Metabolites with Biomedical Significance”. Phytochemical Genomics (2023): 591-604.
94. Yu Y., et al. “Plant noncoding RNAs: hidden players in development and stress responses”. Annual Review of Cell and Developmental Biology 35 (2019): 407-431.
95. Xie Z., et al. “Expression of microRNAs and its regulation in plants”. Seminars in Cell and Developmental Biology 21 (2010): 790-797.
96. Gualtieri C., et al. “Plant miRNA cross-kingdom transfer targeting parasitic and mutualistic organisms as a tool to advance modern agriculture”. Frontiers in Plant Science 11 (2020): 930.
97. de Felippes FF. “Gene regulation mediated by microRNA-triggered secondary small RNAs in plants”. Plants (Basel, Switzerland) 8 (5 (2019): 112.
98. Fei Q., et al. “Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks”. Plant Cell 25 (2013): 2400-2415.
99. Franco-Zorrilla JM., et al. “Target mimicry provides a new mechanism for regulation of microRNA activity”. Nature Genetics 39 (2007): 1033-1037.
100. Heo JB and Sung S. “Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA”. Science 331 (2011): 76-79.
101. Matzke MA and Mosher RA. “RNA-directed DNA methylation: an epigenetic pathway of increasing complexity”. Nature Reviews Genetics 15 (2011): 394-408.
102. Zuo J., et al. “Deciphering the roles of circRNAs on chilling injury in tomato”. Biochemical and Biophysical Research Communications 479 (2016): 132-138.
103. Wang Y., et al. “Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress”. Frontiers in Plant Science 7 (2017): 2024.
104. Tang B., et al. “Genome-wide identification and functional analysis of circRNAs in Zea mays”. bioRxiv (2018).
105. Zhang J., et al. “GreenCircRNA: a database for plant circRNAs that act as miRNA decoys”. Database 2020 (2020): baaa039.
106. Bulgakov VP., et al. “New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs”. Biotechnology Letter 37 (2015): 1719-1727.
107. Gupta OP., et al. “Contemporary understanding of miRNA-based regulation of secondary metabolites biosynthesis in plants”. Frontiers in Plant Science 8 (2017): 374.
108. Adjei M., et al. “MicroRNAs roles in plants secondary metabolism”. Plant Signaling and Behavior 16 (2021): 1915590.
109. Taylor LP., et al. “Flavonoids as developmental regulators”. Current Opinion on Plant Biology 8 (2005): 317-323.
110. Lepiniec L., et al. “Genetics and biochemistry of seed flavonoids”. Annual Reviews Plant Biology 57 (2006): 405-430.
111. Santelia D., et al. “Flavonoids redirect PIN-mediated polar auxin fluxes during root gravitropic responses”. Journal of Biological Chemistry 283 (2008): 31218-31226.
112. Buer CS., et al. “Flavonoids: new roles for old molecules”. Journal of Integrative Plant Biology 52 (2010): 98-111.
113. Sharma D., et al. “MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development”. Plant Physiology 171 (2016): 944-959.
114. Kumar P., et al. “Transcriptomes of Podophyllum hexandrum unravel candidate miRNAs and their association with the biosynthesis of secondary metabolites”. Journal of Plant Biochemistry and Biotechnology 27 (2018): 46-54.
115. Biswas S., et al. “Deep sequencing unravels methyl jasmonate responsive novel miRNAs in Podophyllum hexandrum”. Journal of Plant Biochemistry and Biotechnology 31 (2021): 511-523.
116. Yang R., et al. “Small RNA deep sequencing reveals the important role of microRNAs in the halophyte Halostachys capsica”. Plant Biotechnology Journal 13 (2015): 395-408.
117. Dudareva N., et al. “Biosynthesis, function and metabolic engineering of plant volatile organic compounds”. New Phytology 198 (2013): 16-32.
118. Legrand S., et al. “One-step identification of conserved miRNAs, their targets, potential transcription factors and effector genes of complete secondary metabolism pathways after 454 pyrosequencing of calyx cDNAs from the Labiate Salvia sclarea L”. Gene 450 (2009): 55-62.
119. Kurek JKE-J. “Ch. 1: Alkaloids-their importance in nature and for human life”. In: Introductory. IntechOpen, Rijeka (2019).
120. Gutierrez C., et al. “Identification of microRNAs from medicinal plant Murraya koenigii by high-throughput sequencing and their functional implications in secondary metabolite biosynthesis”. Plan Theory1 (2021).
121. Tirumalai V., et al. “miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes”. Journal of Experimental Botany 70 (2019): 4775-4792.
122. Deng Y and Lu S. “Biosynthesis and regulation of phenylpropanoids in plants”. Critical Reviews in Plant Sciences 36 (2017): 257-290.
123. Luo Q-J., et al. “An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis”. Plant Molecular Biology 80 (2012): 117-129.
124. Guan X., et al. “miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development”. Nature Communication 5 (2012): 3050.
125. Jiang N., et al. “Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism”. Nature Communication 11 (2020): 2456.
126. Jyothsna S., et al. “Regulatory Noncoding RNAs: An Emerging Paradigm for Understanding Phytochemical Biosynthesis and Functioning”. Phytochemical Genomics (2023): 605-626.
127. Jha UC., et al. “Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation”. BMC Plant Biology 20 (2020): 466.
128. Xie J and Fan L. “Nicotine biosynthesis is regulated by two more layers: small and long nonprotein-coding RNAs”. Plant Signaling and Behavior 11 (2016): e1184811.
129. Zhang G., et al. “Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening”. DNA Research 25 (2018): 465-476.
130. Kalhori MR., et al. “Regulation of long non-coding RNAs by plant secondary metabolites: a novel anticancer therapeutic approach”. Cancers 6 (2021): 1274.
131. Zhang ZJ. “Artificial trans-acting small interfering RNA: a tool for plant biology study and crop improvements”. Planta 239 (2014): 1139-1146.
132. Samad AFA., et al. “MicroRNA and transcription factor: key players in plant regulatory network”. Frontiers in Plant Science 8 (2017): 565.
133. Sanan-Mishra N., et al. “Secondary siRNAs in plants: biosynthesis, various functions, and applications in virology”. Frontiers in Plant Science 12 (2021): 610283.
134. Shafrin F., et al. “Artificial miRNA-mediated down-regulation of two monolignoid biosynthetic genes (C3H and F5H) cause reduction in lignin content in jute”. Plant Molecular Biology 89 (2015): 511-527.
135. Misra P., et al. “Modulation of transcriptome and metabolome of tobacco by Arabidopsis transcription factor, AtMYB12, leads to insect resistance”. Plant Physiology 152 (2012): 2258-2268.
136. Kaur S., et al. “Reduction in carotenoid levels in the marine diatom Phaeodactylum tricornutum by artificial microRNAs targeted against the endogenous phytoene synthase gene”. Marine Biotechnology 17 (2015): 1-7.
137. Tran Q-G., et al. “Enhancement of β-carotene production by regulating the autophagy-carotenoid biosynthesis seesaw in Chlamydomonas reinhardtii”. Bioresource Technology 292 (2019): 121937.
138. Yao Q., et al. “The roles of microRNAs in epigenetic regulation”. Current Opinion in Chemical Biology 51 (2019): 11-17.
139. Sundaram GM. “Dietary non-coding RNAs from plants: fairy tale or treasure?” Non-coding RNA Research 4 (2019): 63-68.
140. Schwab R., et al. “Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana”. PLoS One 4 (2009): e5980.
141. Cisneros AE and Carbonell A. “Artificial small RNA-based silencing tools for antiviral resistance in plants”. Plan Theory 6 (2020): 669.
142. Carbonell A., et al. “Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance”. Plant Journal 4 (2019).
143. Townshend RJL., et al. “Geometric deep learning of RNA structure”. Science 373 (2021): 1047-1051.
144. Carbonell A. “Secondary small interfering RNA-based silencing tools in plants: an update”. Frontiers in Plant Science 10 (2019): 687.

Citation

Citation: Tanmay Ghosh and Rishin Bhattacharyya. “RNAi Silencing and the Modification of Plant Natural Product Pathways". Acta Scientific Microbiology 9.2 (2026): 17-46.

Copyright

Copyright: © 2026 Tanmay Ghosh and Rishin Bhattacharyya. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.