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Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses

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Abstract

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules and products of primary miRNAs that regulate the target gene expression. Homology-based approaches were employed to identify miRNAs and their targets in Cestrum nocturnum L. and Cestrum diurnum L. A total of 32 and 12 miRNA candidates were identified in C. nocturnum and C. diurnum. These miRNAs belong to 26 and 10 miRNA families and regulate 1024 and 1007 target genes in C. nocturnum, and C. diurnum, respectively. The functional roles of these miRNAs have not been earlier elucidated in Cestrum. MiR815a, miR849, miR1089 and miR172 have a strong propensity to target genes controlling phytochrome-interacting factor 1 (PIF1), ubiquitin-specific protease 12 (UBP12), leucine-rich repeat (LRR) protein kinase and GAI, RGA, SCR (GRAS) family transcription factor in C. nocturnum. While miR5205a, miR1436 and miR530 regulate PATATIN-like protein 6 (PLP6), PHD finger transcription factor and myb domain protein 48 (MYB48) in C. diurnum. Overall, these miRNAs have regulatory responses in biotic and abiotic stresses in both plant species. Eight putative miRNAs and their target genes were selected for qRT-PCR validation. The validated results suggested the importance of miR815a, miR849, miR5205a, miR1089, miR172, miR1436, and miR530 in exerting control over stress responses in C. nocturnum and C. diurnum.

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References

  • Ahmad VU, Baqai FT, Fatima I, Ahmad R (1991) A spirostanol glycoside from Cestrum nocturnum. Phytochemistry 30:3057–3061

    Article  CAS  PubMed  Google Scholar 

  • Al-Reza SM, Rahman A, Ahmed Y, Kang SC (2010a) Inhibition of plant pathogens in vitro and in vivo with essential oil and organic extracts of Cestrum nocturnum L. Pestic Biochem Phys 96:86–92

    Article  CAS  Google Scholar 

  • Al-Reza SM, Rahman A, Cho YS, Kang SC (2010b) Chemical composition and antioxidant activity of essential oil and organic extracts of Cestrum nocturnum L. J Essent Oil Bear Pl 13:615–624

    Article  CAS  Google Scholar 

  • Al-Reza SM, Rahman A, Kang SC (2009) Chemical composition and inhibitory effect of essential oil and organic extracts of Cestrum nocturnum L. on food-borne pathogens. Int J Food Sci Tech 44:1176–1182

    Article  CAS  Google Scholar 

  • Ali M, Qadir MI, Saleem M, Janbaz KH, Gul H, Hussain L, Ahmad B (2013) Hepatoprotective potential of Convolvulus arvensis against paracetamol-induced hepatotoxicity. Bangl J Pharmacol 8:300–304

    Google Scholar 

  • An J, Li Q, Yang J, Zhang G, Zhao Z, Wu Y, Wang Y, Wang W (2019) Wheat F-box protein TaFBA1 positively regulates plant drought tolerance but negatively regulates stomatal closure. Front Plant Sci 10:1242

    Article  PubMed  PubMed Central  Google Scholar 

  • Andrews S (2017) FastQC: a quality control tool for high throughput sequence data. 2010

  • Ashrafi-Dehkordi E, Alemzadeh A, Tanaka N, Razi H (2018) Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato. PeerJ 6:e4631

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bano N, Fakhrah S, Mohanty CS, Bag SK (2021) Genome-wide identification and evolutionary analysis of gossypium tubby-like protein (TLP) gene family and expression analyses during salt and drought stress. Front Plant Sci 12:667929

    Article  PubMed  PubMed Central  Google Scholar 

  • Barozai MYK, Baloch IA, Din M (2012) Identification of MicroRNAs and their targets in Helianthus. Mol Biol Rep 39:2523–2532

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharjee I, Ghosh A, Chandra G (2005) Antimicrobial activity of the essential oil of Cestrum diurnum (L.) (Solanales: Solanaceae). Afr J Biotechnol 4:371–374

    CAS  Google Scholar 

  • Bielach A, Hrtyan M, Tognetti VB (2017) Plants under stress: involvement of auxin and cytokinin. Int J Mol Sci 18:1427

    Article  PubMed Central  CAS  Google Scholar 

  • Boke H, Ozhuner E, Turktas M, Parmaksiz I, Ozcan S, Unver T (2015) Regulation of the alkaloid biosynthesis by miRNA in opium poppy. Plant Biotechnol J 13:409–420

    Article  CAS  PubMed  Google Scholar 

  • Borges CV, Minatel IO, Gomez-Gomez HA, Lima GPP (2017) Medicinal plants: influence of environmental factors on the content of secondary metabolites. In: Medicinal plants and environmental challenges. Springer, New York, pp 259–277

  • Buchbauer G, Jirovetz L, Kaul VK (1995) Volatiles of the absolute of Cestrum nocturnum L. J Essent Oil Res 7:5–9

    Article  CAS  Google Scholar 

  • Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR et al (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen XM (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025

    Article  CAS  PubMed  Google Scholar 

  • Cheng C, Zhong Y, Wang Q, Cai Z, Wang D, Li C (2019) Genome-wide identification and gene expression analysis of SOS family genes in tuber mustard (Brassica juncea var. tumida). PLoS ONE 14:e0224672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng L, Shafiq S, Xu W, Sun Q (2018) EARLY FLOWERING IN SHORT DAYS (EFS) regulates the seed size in Arabidopsis. Sci China Life Sci 61:214–224

    Article  PubMed  Google Scholar 

  • Chory J, Chatterjee M, Cook RK, Elich T, Fankhauser C, Li J, Nagpal P, Neff M, Pepper A, Poole D et al (1996) From seed germination to flowering, light controls plant development via the pigment phytochrome. Proc Natl Acad Sci USA 93:12066–12071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cristina MS, Petersen M, Mundy J (2010) Mitogen-activated protein kinase signaling in plants. Annu Rev Plant Biol 61:621–649

    Article  CAS  Google Scholar 

  • Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cui X, Lu F, Li Y, Xue Y, Kang Y, Zhang S, Qiu Q, Cui X, Zheng S, Liu B et al (2013) Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Plant Physiol 162:897–906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res 46:W49–W54

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Lorenzo L, Merchan F, Laporte P, Thompson R, Clarke J, Sousa C, Crespi M (2009) A novel plant leucine-rich repeat receptor kinase regulates the response of Medicago truncatula roots to salt stress. Plant Cell 21:668–680

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dhandapani V, Ramchiary N, Paul P, Kim J, Choi SH, Lee J, Hur Y, Lim YP (2011) Identification of potential microRNAs and their targets in Brassica rapa L. Mol Cells 32:21–37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA (2017) Functional roles of microRNAs in agronomically important plants-potential as targets for crop improvement and protection. Front Plant Sci 8:378

    Article  PubMed  PubMed Central  Google Scholar 

  • Dong NQ, Sun YW, Guo T, Shi CL, Zhang YM, Kan Y, Xiang YH, Zhang H, Yang YB, Li YC et al (2020) UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat Communic 11:1

    CAS  Google Scholar 

  • Doubnerová V, Ryslava H (2013) Roles of Hsp70 in plant abiotic stress. In: Molecular approaches in plant abiotic stress. CRC Press, Boca Raton

  • Gao Y, Wu MQ, Zhang MJ, Jiang W, Ren XY, Liang EX, Zhang DP, Zhang CQ, Xiao N, Li Y et al (2018) A maize phytochrome-interacting factors protein ZmPIF1 enhances drought tolerance by inducing stomatal closure and improves grain yield in Oryza sativa. Plant Biotechnol J 16:1375–1387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghosh A, Chandra G (2006) Biocontrol efficacy of Cestrum diurnum L. (Solanaceae: Solanales) against the larval forms of Anopheles stephensi. Nat Prod Res 20:371–379

    Article  CAS  PubMed  Google Scholar 

  • Golldack D, Li C, Mohan H, Probst N (2013) Gibberellins and abscisic acid signal crosstalk: living and developing under unfavorable conditions. Plant Cell Rep 32:1007–1016

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez JE, Marketon MM (2003) Quorum sensing in nitrogen-fixing rhizobia. Microbiol Mol Biol R 67:574

    Article  CAS  Google Scholar 

  • Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342:129–138

    CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154-158

    Article  CAS  PubMed  Google Scholar 

  • Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM (2016) Structural and functional analysis of the GRAS Gene family in grapevine indicates a role of GRAS proteins in the control of development and stress responses. Front Plant Sci 7:353

    Article  PubMed  PubMed Central  Google Scholar 

  • Gutierrez-Luna FM, Hernandez-Dominguez EE, Valencia-Turcotte LG, Rodriguez-Sotres R (2018) Review: “Pyrophosphate and pyrophosphatases in plants, their involvement in stress responses and their possible relationship to secondary metabolism.” Plant Sci 267:11–19

    Article  CAS  PubMed  Google Scholar 

  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512

    Article  CAS  PubMed  Google Scholar 

  • Hashimoto Y, Akiyama Y, Yuasa Y (2013) Multiple-to-multiple relationships between MicroRNAs and target genes in gastric cancer. PLoS ONE 8:e622589

    Article  Google Scholar 

  • Hossain MS, Hoang NT, Yan Z, Toth K, Meyers BC, Stacey G (2019) Characterization of the spatial and temporal expression of two soybean miRNAs Identifies SCL6 as a novel regulator of soybean nodulation. Front Plant Sci 10

  • Islam A, Leung S, Nikmatullah A, Dijkwel PP, McManus MT (2017) Kunitz proteinase inhibitors limit water stress responses in white clover (Trifolium repens L.) plants. Front Plant Sci 8:1683

    Article  PubMed  PubMed Central  Google Scholar 

  • Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jalmi SK, Sinha AK (2015) ROS mediated MAPK signaling in abiotic and biotic stress- striking similarities and differences. Front Plant Sci 6:769

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  • Jung JH, Seo YH, Seo PJ, Reyes JL, Yun J, Chua NH, Park CM (2007) The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19:2736–2748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361

    Article  CAS  PubMed  Google Scholar 

  • Kantar M, Lucas SJ, Budak H (2011) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233:471–484

    Article  CAS  PubMed  Google Scholar 

  • Karpinska M, Borowski J, Danowska-Oziewicz M (2001) The use of natural antioxidants in ready-to-serve food. Food Chem 72:5–9

    Article  CAS  Google Scholar 

  • Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J: Cell Mol Biol 38:823–839

    Article  CAS  Google Scholar 

  • Kim JY, Song JT, Seo HS (2017) COP1 regulates plant growth and development in response to light at the post-translational level. J Exp Bot 68:4737–4748

    Article  CAS  PubMed  Google Scholar 

  • Kleinwächter M, Selmar D (2014) Influencing the product quality by applying drought stress during the cultivation of medicinal plants. Physiological mechanisms and adaptation strategies in plants under changing environment, pp 57–73

  • Krckova Z, Kocourkova D, Danek M, Brouzdova J, Pejchar P, Janda M, Pokotylo I, Ott PG, Valentova O, Martinec J (2018) The Arabidopsis thaliana non-specific phospholipase C2 is involved in the response to Pseudomonas syringae attack. Ann Bot-Lond 121:297–310

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • La Camera S, Balague C, Gobel C, Geoffroy P, Legrand M, Feussner I, Roby D, Heitz T (2009) The Arabidopsis Patatin-like protein 2 (PLP2) plays an essential role in cell death execution and differentially affects biosynthesis of oxylipins and resistance to pathogens. Mol Plant Microbe 22:469–481

    Article  CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Li P, Zhang B, Su TB, Li PR, Xin XY, Wang WH, Zhao XY, Yu YJ, Zhang DH, Yu SC et al (2018) BrLAS, a GRAS transcription factor from Brassica rapa, is involved in drought stress tolerance in transgenic Arabidopsis. Front Plant Sci 9

  • Liao YR, Hu CQ, Zhang XW, Cao XF, Xu ZJ, Gao XL, Li LH, Zhu JQ, Chen RJ (2017) Isolation of a novel leucine-rich repeat receptor-like kinase (OsLRR2) gene from rice and analysis of its relation to abiotic stress responses. Biotechnol Biotec Eq 31:51–57

    Article  CAS  Google Scholar 

  • Lim CW, Baek W, Lim J, Hong E, Lee SC (2021) Pepper ubiquitin-specific protease, CaUBP12, positively modulates dehydration resistance by enhancing CaSnRK2.6 stability. Plant J: Cell Mol Biol 107:1148

    Article  CAS  Google Scholar 

  • Lin CC, Chu CF, Liu PH, Lin HH, Liang SC, Hsu WE, Lin JS, Wang HM, Chang LL, Chien CT et al (2011) Expression of an Oncidium gene encoding a patatin-like protein delays flowering in Arabidopsis by reducing gibberellin synthesis. Plant Cell Physiol 52:421–435

    Article  CAS  PubMed  Google Scholar 

  • Lin JS, Kuo CC, Yang IC, Tsai WA, Shen YH, Lin CC, Liang YC, Li YC, Kuo YW, King YC et al (2018) MicroRNA160 modulates plant development and heat shock protein gene expression to mediate heat tolerance in Arabidopsis. Front Plant Sci 9

  • Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14:836–843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu M, Lu S (2016) Plastoquinone and ubiquinone in plants: biosynthesis, physiological function and metabolic engineering. Front Plant Sci 7:1898

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu ZB, Zhang JH, Gao JH, Li YN (2018) MicroRNA-4728 mediated regulation of MAPK oncogenic signaling in papillary thyroid carcinoma. Saudi J Biol Sci 25:986–990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma SS, Bohnert HJ (2007) Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 8

  • Ma ZX, Hu XP, Cai WJ, Huang WH, Zhou X, Luo Q, Yang HQ, Wang JW, Huang JR (2014) Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. Plos Genet 10:e1004519

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mello JRB (2003) Calcinosis - calcinogenic plants. Toxicon 41:1–12

    Article  CAS  PubMed  Google Scholar 

  • Miura K, Renhu N, Suzaki T (2020) The PHD finger of Arabidopsis SIZ1 recognizes trimethylated histone H3K4 mediating SIZ1 function and abiotic stress response. Commun Biol 3

  • Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 61:165–177

    Article  CAS  PubMed  Google Scholar 

  • Moon J, Zhu L, Shen H, Huq E (2008) PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis. Proc Natl Acad Sci USA 105:9433–9438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182-185

    Article  PubMed  PubMed Central  Google Scholar 

  • Nawaz MS, Arshad A, Rajput L, Fatima K, Ullah S, Ahmad M, Imran A (2020) Growth-stimulatory effect of quorum sensing signal molecule N-acyl-homoserine lactone-producing multi-trait Aeromonas spp. on wheat genotypes under salt stress. Front Microbiol 11

  • Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263

    Article  CAS  PubMed  Google Scholar 

  • Panda D, Dehury B, Sahu J, Barooah M, Sen P, Modi MK (2014) Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 537:333–342

    Article  CAS  PubMed  Google Scholar 

  • Park SH, Jeong JS, Seo JS, Park BS, Chua NH (2019) Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. New Phytol 223:1447–1460

    Article  CAS  PubMed  Google Scholar 

  • Patanun O, Lertpanyasampatha M, Sojikul P, Viboonjun U, Narangajavana J (2013) Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.). Mol Biotechnol 53:257–269

    Article  CAS  PubMed  Google Scholar 

  • Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A et al (2015) FunRich: an open access standalone functional enrichment and interaction network analysis tool. Proteomics 15:2597–2601

    Article  CAS  PubMed  Google Scholar 

  • Peterson SM, Thompson JA, Ufkin ML, Sathyanarayana P, Liaw L, Congdon CB (2014) Common features of microRNA target prediction tools. Front Genet 5

  • Piya S, Kihm C, Rice JH, Baum TJ, Hewezi T (2017) Cooperative regulatory functions of miR858 and MYB83 during cyst nematode parasitism. Plant Physiol 174:1897–1912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prema T, Raghuramulu N (1994) Free vitamin D3 metabolites in Cestrum diurnum leaves. Phytochemistry 37:677–681

    Article  CAS  Google Scholar 

  • Ravindran P, Yong SY, Mohanty B, Kumar PP (2020) An LRR-only protein regulates abscisic acid-mediated abiotic stress responses during Arabidopsis seed germination. Plant Cell Rep 39:909

    Article  CAS  PubMed  Google Scholar 

  • Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592–606

    Article  CAS  PubMed  Google Scholar 

  • Schikora A, Schenk ST, Hartmann A (2016) Beneficial effects of bacteria-plant communication based on quorum sensing molecules of the N-acyl homoserine lactone group. Plant Mol Biol 90:605–612

    Article  CAS  PubMed  Google Scholar 

  • Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101–1108

    Article  CAS  PubMed  Google Scholar 

  • Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of MicroRNAs on the plant transcriptome. Dev Cell 8:517–527

    Article  CAS  PubMed  Google Scholar 

  • Sharma A, Shanker C, Tyagi LK, Singh M, Rao CV (2008) Herbal medicine for market potential in India: an overview. Acad J Plant Sci 1:26–36

    Google Scholar 

  • Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK (2016) MicroRNA858 Is a potential regulator of phenylpropanoid pathway and plant development. Plant Physiol 171:944–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi HZ, Ishitani M, Kim CS, Zhu JK (2000) The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. Proc Natl Acad Sci USA 97:6896–6901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shim JS, Kubota A, Imaizumi T (2017) Circadian clock and photoperiodic flowering in Arabidopsis: CONSTANS is a hub for signal integration. Plant Physiol 173:5–15

    Article  CAS  PubMed  Google Scholar 

  • Shin B, Choi G, Yi H, Yang S, Cho I, Kim J, Lee S, Paek NC, Kim JH, Song PS (2002) AtMYB21, a gene encoding a flower-specific transcription factor, is regulated by COP1. Plant J 30:23–32

    Article  CAS  PubMed  Google Scholar 

  • Shukla LI, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochem Biophys Acta 1779:743–748

    CAS  PubMed  Google Scholar 

  • Sinha AK, Jaggi M, Raghuram B, Tuteja N (2011) Mitogen-activated protein kinase signaling in plants under abiotic stress. Plant Signal Behav 6:196–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432

    Article  CAS  PubMed  Google Scholar 

  • Solecka D (1997) Role of phenylpropanoid compounds in plant responses to different stress factors. Acta Physiol Plant 19:257–268

    Article  CAS  Google Scholar 

  • Song H, Guo ZL, Chen T, Sun J, Yang GF. 2018. Genome-wide identification of LRR-containing sequences and the response of these sequences to nematode infection in Arachis duranensis. BMC Plant Biol 18

  • Song XW, Li Y, Cao XF, Qi YJ (2019) MicroRNAs and their regulatory roles in plant–environment interactions. Annu Rev Plant Biol 70:489–525

    Article  CAS  PubMed  Google Scholar 

  • Song YH, Shim JS, Kinmonth-Schultz HA, Imaizumi T (2015) Photoperiodic flowering: time measurement mechanisms in leaves. Annu Rev Plant Biol 66:441–464

    Article  CAS  PubMed  Google Scholar 

  • Soy J, Leivar P, Monte E (2014) PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5. J Exp Bot 65:2925–2936

    Article  PubMed  PubMed Central  Google Scholar 

  • Srikanth A, Schmid M (2011) Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci 68:2013–2037

    Article  CAS  PubMed  Google Scholar 

  • Srivastava S, Singh N, Srivastava G, Sharma A (2017) MiRNA mediated gene regulatory network analysis of Cichorium intybus (chicory). Agri Gene 3:37–45

    Article  Google Scholar 

  • Stark A, Brennecke J, Russell RB, Cohen SM (2003) Identification of Drosophila MicroRNA targets. PLoS Biol 1:397–409

    Article  CAS  Google Scholar 

  • Su G, Morris JH, Demchak B, Bader GD. 2014. Biological network exploration with Cytoscape 3. Current protocols in bioinformatics 47: 8 13 11–24.

  • Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203

    Article  CAS  PubMed  Google Scholar 

  • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P et al (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39:D561–D568

    Article  CAS  PubMed  Google Scholar 

  • Teotia S, Tang G (2015) To bloom or not to bloom: role of microRNAs in plant flowering. Mol Plant 8:359–377

    Article  CAS  PubMed  Google Scholar 

  • Thakur S, Pandit K, Kumar A, Kaur J, Kaur S (2021) Phenylpropanoid biosynthesis and its protective effects against plants stress. Environ Stress Physiol Plants Crop Prod 144

  • Tholl D. 2015. Biosynthesis and biological functions of terpenoids in plants. Biotechnology of isoprenoids, pp 63–106

  • Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W, Su Z (2017) agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res 45:W122–W129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Unver T, Parmaksız I, Dündar E (2010) Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep 29:757–769

    Article  CAS  PubMed  Google Scholar 

  • Usman MG, Rafii MY, Martini MY, Yusuff OA, Ismail MR, Miah G (2017) Molecular analysis of Hsp70 mechanisms in plants and their function in response to stress. Biotechnol Genet Eng 33:26–39

    Article  CAS  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant MicroRNAs. Cell 136:669–687

    Article  CAS  PubMed  Google Scholar 

  • Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204–2216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang M, Wang Q, Wang B (2012) Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS ONE 7:e33696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang PC, Hsu CC, Du YY, Zhu PP, Zhao CZ, Fu X, Zhang CG, Paez JS, Macho AP, Tao WA et al (2020a) Mapping proteome-wide targets of protein kinases in plant stress responses. Proc Natl Acad Sci USA 117:3270–3280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang TT, Yu TF, Fu JD, Su HG, Chen J, Zhou YB, Chen M, Guo J, Ma YZ, Wei WL et al (2020b) Genome-wide analysis of the GRAS gene family and functional identification of GmGRAS37 in drought and salt tolerance. Front Plant Sci 11:604690

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Wang QQ, Liu ML, Bo C, Wang X, Ma Q, Cheng BJ, Cai RH (2017) Overexpression of a maize MYB48 gene confers drought tolerance in transgenic arabidopsis plants. J Plant Biol 60:612–621

    Article  CAS  Google Scholar 

  • Wasserman R, Corradino R, Krook L, Hughes M, Haussler M (1976) Studies on the 1α, 25-dihydroxycholecalciferol-like activity in a calcinogenic plant, Cestrum diurnum, in the chick. J Nutr 106:457–465

    Article  CAS  PubMed  Google Scholar 

  • Wei W, Zhang YQ, Tao JJ, Chen HW, Li QT, Zhang WK, Ma B, Lin Q, Zhang JS, Chen SY (2015) The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis. Plant J 81:871–883

    Article  CAS  PubMed  Google Scholar 

  • Xin MM, Wang Y, Yao YY, Song N, Hu ZR, Qin DD, Xie CJ, Peng HR, Ni ZF, Sun QX (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 Biol 11

  • Xiong HY, Li JJ, Liu PL, Duan JZ, Zhao Y, Guo X, Li Y, Zhang HL, Ali J, Li ZC (2014) Overexpression of OsMYB48-1, a Novel MYB-related transcription factor, enhances drought and salinity tolerance in rice. PLoS ONE 9

  • Xu K, Chen SJ, Li TF, Ma XS, Liang XH, Ding XF, Liu HY, Luo LJ. 2015a. OsGRAS23, a rice GRAS transcription factor gene, is involved in drought stress response through regulating expression of stress-responsive genes. BMC plant biology 15.

  • Xu Y, Chu L, Jin Q, Wang Y, Chen X, Zhao H, Xue Z (2015b) Transcriptome-wide identification of miRNAs and their targets from Typha angustifolia by RNA-Seq and their response to cadmium stress. PLoS ONE 10

  • Yamamoto YY, Matsui M, Ang LH, Deng XW (1998) Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis. Plant Cell 10:1083–1094

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang XQ, Zhang LC, Yang YZ, Schmid M, Wang YW (2021) miRNA mediated regulation and interaction between plants and pathogens. Int J Mol Sci 22:2913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Younger ST, Pertsemlidis A, Corey DR (2009) Predicting potential miRNA target sites within gene promoters. Bioorg Med Chem Lett 19:3791–3794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan N, Yuan S, Li Z, Zhou M, Wu P, Hu Q, Mendu V, Wang L, Luo H (2018) STRESS INDUCED FACTOR 2, a leucine-rich repeat kinase regulates basal plant pathogen defense. Plant Physiol 176:3062–3080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeng CY, Wang WQ, Zheng Y, Chen X, Bo WP, Song S, Zhang WX, Peng M (2010) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Res 38:981–995

    Article  CAS  PubMed  Google Scholar 

  • Zhai JX, Jeong DH, De Paoli E, Park S, Rosen BD, Li YP, Gonzalez AJ, Yan Z, Kitto SL, Grusak MA et al (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Gene Dev 25:2540–2553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang B, Liu J, Yang ZE, Chen EY, Zhang CJ, Zhang XY, Li FG (2018) Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L. BMC Genomics 19

  • Zhang B, Pan X, Cox S, Cobb G, Anderson T (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci CMLS 63:246–254

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Pan X, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229:161–182

    Article  CAS  PubMed  Google Scholar 

  • Zhang JY, Xu YY, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10

  • Zhao C, Zayed O, Yu Z, Jiang W, Zhu P, Hsu CC, Zhang L, Tao WA, Lozano-Duran R, Zhu JK (2018a) Leucine-rich repeat extensin proteins regulate plant salt tolerance in Arabidopsis. Proc Natl Acad Sci USA 115:13123–13128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors acknowledge HPC facility, CSIR-4PI, Bangaluru and CSIR-National Botanical Research Institute Lucknow, India for providing facilities. We duly acknowledge Dr. Sanchita to design the work and Dr. Yogita Deshmukh for editing the English text of manuscript. The manuscript number is provided by the institute is CSIR- NBRI_MS/2020/06/09.

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Authors and Affiliations

  1. CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India

    Nasreen Bano, Shafquat Fakhrah, Sagar Prasad Nayak, Sumit Kumar Bag & Chandra Sekhar Mohanty

  2. Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

    Nasreen Bano, Sagar Prasad Nayak, Sumit Kumar Bag & Chandra Sekhar Mohanty

  3. Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India

    Shafquat Fakhrah

  4. Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India

    Sumit Kumar Bag

  5. Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, India

    Chandra Sekhar Mohanty

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  1. Nasreen Bano
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  2. Shafquat Fakhrah
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  3. Sagar Prasad Nayak
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  4. Sumit Kumar Bag
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  5. Chandra Sekhar Mohanty
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Contributions

NB carried out the bioinformatics analysis, design, and drafted the manuscript. SF and SPN performed quantitative expression analysis. SKB and CSM participated to supervise the study. All the authors read and approved the final manuscript.

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Correspondence to Sumit Kumar Bag or Chandra Sekhar Mohanty.

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Bano, N., Fakhrah, S., Nayak, S.P. et al. Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses. Physiol Mol Biol Plants 28, 31–49 (2022). https://doi.org/10.1007/s12298-022-01127-1

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  • DOI: https://doi.org/10.1007/s12298-022-01127-1

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