Abstract
Since time immemorial, humans utilize plants for various needs such as food, shelter, fuelwood, and medicine. Plants exhibit medicinal properties due to the presence of several classes of phytochemicals, especially secondary metabolites, also known as specialized metabolites (SMs). Plants are chemical factories and many important drugs used today are derived from the plants or plant-inspired semi-biosynthetic pathways. Large numbers of plants are being increasingly explored for medicinally important specialized metabolites because there has been an increase in the interest in bioprospecting natural sources of more drugs. However, current bioprospecting approaches are not sustainable. Therefore, modern approaches can be used for the characterization of medicinally important plants for metabolites/phytochemicals present in them and for the validation of their medicinal properties in treating several serious diseases. Recent decades have seen the emergence of new technologies which can be deployed to characterize the phytochemicals present in the plants on a large scale. The genetic biosynthetic pathways of the plants can also be traced using high-throughput technologies such as genomics, proteomics, metabolomics, and transcriptomics. Several studies aim to characterize biosynthetic pathways of phytochemicals, and efforts are on identifying genes, proteins, and metabolomes associated with a particular metabolite. All this has led to an emergence of an entirely new discipline known as phytochemical genomics, which involves the integration of multi-omics approaches, such as genomics, transcriptomics, proteomics, and metabolomics intending to decipher gene-protein-metabolite networks. This chapter introduces the concept of phytochemical genomics, various techniques/technologies, and approaches that are used in phytochemical genomics and some of the examples of medicinal plants, where these technologies have been successfully utilized. This chapter further delves into linking gene editing technologies with omics information for the improvement of medicinal plants.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Abbas MST (2018) Genetically engineered (modified) crops (Bacillus thuringiensis crops) and the world controversy on their safety. Egypt J Biol Pest Control 28:52. https://doi.org/10.1186/s41938-018-0051-2
Abdallah NA, Prakash CS, McHughen AG (2015) Genome editing for crop improvement: challenges and opportunities. GM Crops Food 6(4):183–205. https://doi.org/10.1080/21645698.2015.1129937
Adrio JL, Demain AL (2006) Genetic improvement of processes yielding microbial products. FEMS Microbiol Rev 30(2):187–214. https://doi.org/10.1111/j.1574-6976.2005.00009.x
Adrio J-L, Demain AL (2010) Recombinant organisms for production of industrial products. Bioeng Bugs 1(2):116–131. https://doi.org/10.4161/bbug.1.2.10484
Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S (2011) KNApSAcK family databases: integrated metabolite–plant species databases for multifaceted plant research. Plant Cell Physiol 53(2). https://doi.org/10.1093/pcp/pcr165
Agapito-Tenfen SZ, Okoli AS, Bernstein MJ, Wikmark OG, Myhr AI (2018) Revisiting risk governance of GM plants: the need to consider new and emerging gene-editing techniques. Front Plant Sci 9. https://doi.org/10.3389/fpls.2018.01874
Agarwal V, Chauhan BM (1988) A study on composition and hypolipidemic effect of dietary fibre from some plant foods. Plant Foods Hum Nutr 38(2):189–197. https://doi.org/10.1007/bf01091723
Aghaei K, Komatsu S (2013) Crop and medicinal plants proteomics in response to salt stress. Front Plant Sci 4:8. https://doi.org/10.3389/fpls.2013.00008
Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R (2013) A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues: a decade of plant proteomics and mass spectrometry. Mass Spectrom Rev 32(5):335–365. https://doi.org/10.1002/mas.21365
Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong W-J, Jung K-H (2020) A revolution toward gene-editing technology and its application to crop improvement. Int J Mol Sci 21(16):5665. https://doi.org/10.3390/ijms21165665
Aizat WM, Dias DA, Stangoulis JCR, Able JA, Roessner U, Able AJ (2014) Metabolomics of capsicum ripening reveals modification of the ethylene related-pathway and carbon metabolism. Postharvest Biol Technol 89:19–31. https://doi.org/10.1016/j.postharvbio.2013.11.004
Alagoz Y, Gurkok T, Zhang B, Unver T (2016) Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep 6(1):30910. https://doi.org/10.1038/srep30910
Alanazi IO, Benabdelkamel H, Alfadda AA, AlYahya SA, Alghamdi WM, Aljohi HA, Almalik A, Masood A (2016) Proteomic analysis of the protein expression profile in the mature Nigella sativa (Black seed). Appl Biochem Biotechnol 179:1184–1201. https://doi.org/10.1007/s12010-016-2058-z
Alavizadeh SH, Hosseinzadeh H (2014) Bioactivity assessment and toxicity of crocin: a comprehensive review. Food Chem Toxicol 64:65–80. https://doi.org/10.1016/j.fct.2013.11.016
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell, 4th edn. Garland Science, New York
Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Armengaud P, Quilleré I, Cañas R, Tercet-Laforgue T, Hirel B (2012) The use of metabolomics integrated with transcriptomic and proteomic studies for identifying key steps involved in the control of nitrogen metabolism in crops such as maize. J Exp Bot 63:5017–5033. https://doi.org/10.1093/jxb/ers186
Amme S, Rutten T, Melzer M, Sonsmann G, Vissers JPC, Schlesier B, Mock H-P (2005) A proteome approach defines protective functions of tobacco leaf trichomes. Proteomics 5(10):2508–2518. https://doi.org/10.1002/pmic.200401274
Araújo-Lima CF, Paula da Silva Oliveira J, Coscarella IL, Fortes Aiub CA, Felzenszwalb I, Caprini Evaristo GP, Macedo AF (2020) Metabolomic analysis of Cyrtopodium glutiniferum extract by UHPLC-MS/MS and in vitro anti proliferative and genotoxicity assessment. J Ethnopharmacol:112607. https://doi.org/10.1016/j.jep.2020.112607
Aronson JK (2017) Defining ‘nutraceuticals’: neither nutritious nor pharmaceutical. Br J Clin Pharmacol 83(1):8–19. https://doi.org/10.1111/bcp.12935
Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH (2017) Proteomics: technologies and their applications. J Chromatogr Sci 55(2):182–196. https://doi.org/10.1093/chromsci/bmw167
Awang DVC, Dawson BA, Kindack DG, Crompton CW, Heptinstall S (1991) Parthenolide content of feverfew (Tanacetum parthenium) assessed by HPLC and 1H-NMR. J Nat Prod 54(6):1516–1521. https://doi.org/10.1021/np50078a005
Babaoglu M, Davey MR, Power JB, Sporer F, Wink M (2004) Transformed roots of Lupinus mutabilis: induction, culture and isoflavone biosynthesis. Plant Cell Tissue Organ Cult 78:29–36
Baiano A (2014) Recovery of biomolecules from food waste—a review. Molecules 19:14821–14842. https://doi.org/10.3390/molecules190914821
Bais P, Moon SM, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Roth MR, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau BJ, Rhee SY, Dickerson JA (2010) PlantMetabolomics.org: a web portal for plant metabolomics experiments. Plant Physiol 152(4):1807–1816. https://doi.org/10.1104/pp.109.151027
Balint GA (2001) Artemisinin and its derivatives: an important new class of antimalarial agents. Pharmacol Ther 90:261–265
Balunas MJ, Kinghorn AD (2005) Drug discovery from medicinal plants. Life Sci 78(5):431–441. https://doi.org/10.1016/j.lfs.2005.09.012
Barrientos R, Fernández-Galleguillos C, Pastene E, Simirgiotis M, Romero-Parra J, Ahmed S, Echeverría J (2020) Metabolomic analysis, fast isolation of phenolic compounds, and evaluation of biological activities of the bark from Weinmannia trichosperma Cav. (Cunoniaceae). Front Pharmacol 11. https://doi.org/10.3389/fphar.2020.00780
Beaudoin GAW, Facchini PJ (2014) Benzylisoquinoline alkaloid biosynthesis in opium poppy. Planta 240:19–32. https://doi.org/10.1007/s00425-014-2056-8
Beedanagari S, John K (2014) Next generation sequencing. In: Encyclopedia of toxicology, 3rd edn. Academic Press, London, pp 501–503
Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84. https://doi.org/10.1016/j.copbio.2014.11.007
Bellik Y, Boukraa L, Alzahrani HA, Bakhotmah BA, Abdellah F, Hammoudi SM, Iguer-Ouada M (2013) Molecular mechanism underlying anti-inflammatory and anti-allergic activities of phytochemicals: an update. Molecules 18:322–353. https://doi.org/10.3390/molecules18010322
Berg JM, Tymoczko JL, Stryer L (2002) Three-dimensional protein structure can be determined by NMR spectroscopy and X-ray crystallography. In: Biochemistry, 5th edn. W.H. Freeman, New York
Bhambhani S, Lakhwani D, Gupta P, Pandey A, Dhar YV, Bag SK, Asif MH, Trivedi PK (2017) Transcriptome and metabolite analyses in Azadirachta indica identification of genes involved in biosynthesis of bioactive triterpenoids. Sci Rep 7:5043. https://doi.org/10.1038/s41598-017-05291-3
Bhat SA, Manzoor A, Dar IH, Ahmad S (2020) Cereals as functional ingredients in meat and meat products. In: Ahmad S, Al-Shabib N (eds) Functional food products and sustainable health. Springer, Singapore, pp 91–108
Boonmee A, Srisomsap C, Chokchaichamnankit D, Karnchanatat A, Sangvanich P (2011) A proteomic analysis of Curcuma comosa Roxb. rhizomes. Proteome Sci 9(43). https://doi.org/10.1186/1477-5956-9-43
Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33(1):41–52. https://doi.org/10.1016/j.biotechadv.2014.12.006
Boudet AM (2007) Evolution and current status of research in phenolic compounds. Phytochemistry 68(22–24):2722–2735. https://doi.org/10.1016/j.phytochem.2007.06.012
Bourgaud F, Gravot A, Milesi S, Gontier E (2001) Production of plant secondary metabolites: a historical perspective. Plant Sci 161(5):839–851. https://doi.org/10.1016/s0168-9452(01)00490-3
Bowne JB, Erwin TA, Juttner J, Schnurbusch T, Langridge P, Bacic A, Roessner U (2012) Drought responses of leaf tissues from wheat cultivars of differing drought tolerance at the metabolite level. Mol Plant 5(2):418–429. https://doi.org/10.1093/mp/ssr114
Briskin DP (2000) Medicinal plants and phytomedicines. Linking plant biochemistry and physiology to human health. Plant Physiol 124(2):507–514. https://doi.org/10.1104/pp.124.2.507
Bryant L, Patole C, Cramer R (2016) Proteomic analysis of the medicinal plant Artemisia annua: data from leaf and trichome extracts. Data Brief 7:325–331. https://doi.org/10.1016/j.dib.2016.02.038
Bucca A (2018) Role of digoxin in heart failure. In: Sawyer DB, Vasan RS (eds) Encyclopedia of cardiovascular research and medicine. Elsevier, Amsterdam, pp 323–326
Carte BK, DeBrosse C, Eggleston D, Hemling M, Mentzer M, Poehland B, Troupe N, Westley JW (1990) Isolation and characterization of a presumed biosynthetic precursor of camptothecin from extracts of Camptotheca acuminata. Tetrahedron 46(8):2747–2760. https://doi.org/10.1016/s0040-4020(01)88369-1
Casati P, Campi M, Morrow D, Fernandes J, Walbot V (2011) Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize. BMC Genomics 12:321. https://doi.org/10.1186/1471-2164-12-321
Catch JR, Evans EA (1960) Rate of formation of atropine in Atropa belladonna plants. Nature 188(4752):758–759. https://doi.org/10.1038/188758a0
Cequier-Sanchez E, Rodriguez C, Dorta-Guerra R, Ravelo A, Zarate R (2011) Echium acanthocarpum hairy root cultures, a suitable system for polyunsaturated fatty acid studies and production. BMC Biotechnol 11:42. https://doi.org/10.1186/1472-6750-11-42
Čermák T, Baltes NJ, Čegan R, Zhang Y, Voytas DF (2015) High-frequency, precise modification of the tomato genome. Genome Biol 16(1):232. https://doi.org/10.1186/s13059-015-0796-9
Chakraborty P (2018) Herbal genomics as tools for dissecting new metabolic pathways of unexplored medicinal plants and drug discovery. Biochim Open 6:9–16. https://doi.org/10.1016/j.biopen.2017.12.003
Chandler SF, Dodds JH (1983) The effect of phosphate, nitrogen and sucrose on the production of phenolics and solasodine in callus cultures of Solanum laciniatum. Plant Cell Rep 2:205–208. https://doi.org/10.1007/BF00270105
Chekanova JA (2015) Long non-coding RNAs and their functions in plants. Curr Opin Plant Biol 27:207–216. https://doi.org/10.1016/j.pbi.2015.08.003
Chen Z-Y, Jiao R, Ma KY (2008) Cholesterol-lowering nutraceuticals and functional foods. J Agric Food Chem 56:8761–8773. https://doi.org/10.1021/jf801566r
Chen S, Luo H, Li Y, Sun Y, Wu Q, Niu Y, Song J, Lv A, Zhu Y, Sun C, Steinmetz A, Qian Z (2011) 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Rep 30(9):1593–1601. https://doi.org/10.1007/s00299-011-1070-6
Chen G, Wang H, Zhang X, Yang S-T (2014) Nutraceuticals and functional foods in the management of hyperlipidemia. Crit Rev Food Sci 54(9):1180–1201. https://doi.org/10.1080/10408398.2011.629354
Chen RB, Liu J-H, **ao Y, Zhang F, Chen J, Ji Q, Tan X-H, Huang X, Feng H, Huang B-K, Chen WS, Zhang L, Chen S (2015) Deep sequencing reveals the effect of MeJA on scutellarin biosynthesis in Erigeron breviscapus. PLoS One 10(12). https://doi.org/10.1371/journal.pone.0143881
Chen SL, Yu H, Luo HM, Wu Q, Li CF, Steinmetz A (2016) Conservation and sustainable use of medicinal plants: problems, progress, and prospects. Chin Med 11:37. https://doi.org/10.1186/s13020-016-0108-7
Cherukupalli N, Divate M, Mittapelli SR, Khareedu VR, Vudem DR (2016) De novo assembly of leaf transcriptome in the medicinal plant Andrographis paniculata. Front Plant Sci 7. https://doi.org/10.3389/fpls.2016.0120
Choi H-K (2018) Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. Genes Genomics 41:133–146. https://doi.org/10.1007/s13258-018-0751-8
Choi YH, Kim HK, Hazekamp A, Erkelens C, Lefeber AW, Verpoorte R (2004) Metabolomic differentiation of Cannabis sativa cultivars using 1H-NMR spectroscopy and principal component analysis. J Nat Prod 67:953–957. https://doi.org/10.1021/np049919c
Chu I-H, Bodnar JA, Bowman RN, White EL (1997) Determination of vincristine and vinblastine in Catharanthus roseus plants by high performance liquid chromatography/electrospray ionization mass spectrometry. J Liq Chromatogr Relat Technol 20(8):1159–1174. https://doi.org/10.1080/10826079708010966
Cimanga K, De Bruyne T, Pieters L, Claeys M, Vlietinck A (1996) New alkaloids from Cryptolepis sanguinolenta. Tetrahedron Lett 37(10):1703–1706. https://doi.org/10.1016/0040-4039(96)00112-8
Clancy S (2008) DNA transcription. Nat Educ 1(1):41
Clancy S, Brown W (2008) Translation: DNA to mRNA to protein. Nat Educ 1(1):101. https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393/
Cohen J (2020) CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel. Science. https://doi.org/10.1126/science.abf0540. Accessed 13 Dec 2020
Contreras A, Leroy B, Mariage P-A, Wattiez R (2019) Proteomic analysis reveals novel insights into tanshinones biosynthesis in Salvia miltiorrhiza hairy roots. Sci Rep 9:5768. https://doi.org/10.1038/s41598-019-42164-3
Corchete MP, Sanchez JM, Cacho M, Moran M, Fernandez-Tarrago J (1990) Cardenolide content in suspension cell cultures derived from root and leaf callus of Digitalis thapsi L. J Plant Physiol 137:196–200. https://doi.org/10.1016/S0176-1617(11)80081-7
Coskun O (2016) Separation techniques: chromatography. North Clin Istanb 3(2):156–160. https://doi.org/10.14744/nci.2016.32757
Cragg GM, Newman DJ (2005) Plants as a source of anti-cancer agents. J Ethnopharmacol 100(1–2):72–79. https://doi.org/10.1016/j.jep.2005.05.011
da Silva JF, Salic S, Wiedner M, Datlinger P, Essletzbichler P, Hanzl A, Superti-Furga G, Bock C, Winter G, Loizou JI (2019) Genome-scale CRISPR screens are efficient in non-homologous end-joining deficient cells. Sci Rep 9. https://doi.org/10.1038/s41598-019-52078-9
Debnath M, Malik C, Bisen P (2006) Micropropagation: a tool for the production of high quality plant-based medicines. Curr Pharm Biotechnol 7(1):33–49. https://doi.org/10.2174/138920106775789638
Després J-P, Lemieux I, Dagenais G-R, Cantin B, Lamarche B (2000) HDL-cholesterol as a marker of coronary heart disease risk: the Québec cardiovascular study. Atherosclerosis 153(2). https://doi.org/10.1016/s0021-9150(00)00603-1
Doudna JA, Charpentier E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096. https://doi.org/10.1126/science.1258096
Durland J, Ahmadian-Moghadam H (2020) Genetics, mutagenesis. In: StatPearls. StatPearls Publishing, Treasure Island, FL
Efferth T (2019) Biotechnology applications of plant callus cultures. Engineering 5:50–59. https://doi.org/10.1016/j.eng.2018.11.006
Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1–15. https://doi.org/10.1038/hdy.2010.152
Elujoba AA, Odeleye OM, Ogunyemi CM (2005) Traditional medicine development for medical and dental primary health care delivery system in Africa. Afr J Tradit Complement Altern Med 2(1):46–61
Fan R, Li Y, Li C, Zhang Y (2015) Differential microRNA analysis of glandular trichomes and young leaves in Xanthium strumarium L. reveals their putative roles in regulating terpenoid biosynthesis. PLoS One 10(9). https://doi.org/10.1371/journal.pone.0139002
Farag MA, Huhman DV, Dixon RA, Sumner LW (2008) Metabolomics reveals novel pathways and differential mechanistic and elicitor-specific responses in phenylpropanoid and isoflavonoid biosynthesis in Medicago truncatula cell cultures. Plant Physiol 146:387–402. https://doi.org/10.1104/pp.107.108431
Farnsworth NR, Soejarto DD (1988) Global importance of medicinal plants. In: Conservation of medicinal plants. Cambridge University Press, Cambridge, pp 25–52
Farombi EO (2003) African indigenous plants with chemotherapeutic potentials and biotechnological approach to the production of bioactive prophylactic agents. Afr J Biotechnol 2(12):662–671. https://doi.org/10.5897/ajb2003.000-1122
Feng S, Song W, Fu R, Zhang H, Xu A, Li J (2018) Application of the CRISPR/Cas9 system in Dioscorea zingiberensis. Plant Cell Tissue Organ Cult 135(1):133–141. https://doi.org/10.1007/s11240-018-1450-5
Fett-Neto AG, Melanson SJ, Nicholson SA, Pennington JJ, DiCosmo F (1994) Improved taxol yield by aromatic carboxylic acid and amino acid feeding to cell cultures of Taxus cuspidata. Biotechnol Bioeng 44(8):967–971. https://doi.org/10.1002/bit.260440813
Finotello F, Di Camillo B (2015) Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Brief Funct Genomics 14(2):130–142. https://doi.org/10.1093/bfgp/elu035
Froment C, Uttenweiler-Joseph S, Bousquet-Dubouch M-P, Matondo M, Borges J-P, Esmenjaud C, Lacroix C, Monsarrat B, Burlet-Schiltz O (2005) A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity. Proteomics 5(9):2351–2363. https://doi.org/10.1002/pmic.200401281
Fu Y, Li L, Hao S, Guan,R, Fan G, Shi C, Lee SM-Y (2017) Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. GigaScience 6(6):1–5. doi: https://doi.org/10.1093/gigascience/gix033
Fu R, Martin C, Zhang Y (2018) Next-Generation plant metabolic engineering, inspired by an ancient Chinese irrigation system. Mol Plant 11(1):47–57. https://doi.org/10.1016/j.molp.2017.09.002
Gahlan P, Singh HR, Shankar R, Sharma N, Kumari A, Chawla V, Ahuja PS, Kumar S (2012) De novo sequencing and characterization of Picrorhiza kurroa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics 13(1). https://doi.org/10.1186/1471-2164-13-126
Gaj T, Sirk SJ, Shui S, Liu J (2016) Genome-editing technologies: principles and applications. Cold Spring Harb Perspect Biol 8(12):a023754. https://doi.org/10.1101/cshperspect.a023754
Gao SL, Zhu DN, Cai ZH, Jiang Y, Xu DR (1999) Organ culture of a precious Chinese medicinal plant—Fritillaria unibracteata. Plant Cell Tissue Organ Cult 59:197–201. https://doi.org/10.1023/A:1006440801337
Ge Q, Zhang Y, Hua W-P, Wu Y-C, ** X-X, Song S-H, Wang Z-Z (2015) Combination of transcriptomic and metabolomic analyses reveals a JAZ repressor in the jasmonate signaling pathway of Salvia miltiorrhiza. Sci Rep 5. https://doi.org/10.1038/srep14048
Gharari Z, Bagheri K, Danafar H, Sharafi A (2020) Enhanced flavonoid production in hairy root cultures of Scutellaria bornmuelleri by elicitor induced over-expression of MYB7 and FNSП2 genes. Plant Physiol Biochem 148:35–44. https://doi.org/10.1016/j.plaphy.2020.01.002
Glas J, Schimmel B, Alba J, Escobar-Bravo R, Schuurink R, Kant M (2012) Plant glandular trichomes as targets for breeding or engineering of resistance to herbivores. Int J Mol Sci 13(12):17077–17103. https://doi.org/10.3390/ijms131217077
Graves PR, Haystead TAJ (2002) Molecular biologist’s guide to proteomics. Microbiol Mol Biol Rev 66(1):39–63. https://doi.org/10.1128/mmbr.66.1.39-63.2002
Grennan AK (2009) MoTo DB: a metabolic database for tomato. Plant Physiol 151(4):1701–1702. https://doi.org/10.1104/pp.109.900308
Grundy SM (1990) Cholesterol and coronary heart disease future directions. JAMA 264(23):3053–3059. https://doi.org/10.1001/jama.1990.03450230089035
Grusak MA (2002) Phytochemicals in plants: genomics-assisted plant improvement for nutritional and health benefits. Curr Opin Biotechnol 13(5):508–511. https://doi.org/10.1016/s0958-1669(02)00364-6
Gunasekaran B, Gothandam KM (2020) A review on edible vaccines and their prospects. Braz J Med Biol Res 53(2). https://doi.org/10.1590/1414-431x20198749
Hachez C (2017) Plant glandular trichomes: natural cell factories of high biotechnological interest. Plant Physiol 175(1):6–22. https://doi.org/10.1104/pp.17.00727
Hager GL, McNally JG, Misteli T (2009) Transcription dynamics. Mol Cell 35(6):741–753. https://doi.org/10.1016/j.molcel.2009.09.005
Hall RD (2006) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169(3):453–468. https://doi.org/10.1111/j.1469-8137.2005.01632.x
Hall R, Beale M, Fiehn O, Hardy N, Sumner L, Bino R (2002) Plant metabolomics. Plant Cell 14(7):1437–1440. https://doi.org/10.1105/tpc.140720
Hansen LL, Jaroszewski JW (1996) Effect of gossypol on cultured TM3 leydig and TM4 sertoli cells: 31P and 23Na NMR study. NMR Biomed 9(2):72–78. https://doi.org/10.1002/(sici)1099-1492(199604)9:2<72::aid-nbm406>3.0.co;2-3
Hao DC, **ao PG (2015) Genomics and evolution in traditional medicinal plants: road to a healthier life. Evol Bioinforma 11:197–212. https://doi.org/10.4137/EBO.S31326
Hao D, Ma P, Mu J, Chen S, **ao P, Peng Y, Huo L, Xu L, Sun C (2012) De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Sci China Life Sci 55(5):452–466. https://doi.org/10.1007/s11427-012-4319-6
Harborne JB (1973) Methods of plant analysis. In: Phytochemical methods: a guide to modern techniques of plant analysis. Fakenham Press Limited, Norfolk, p 27
Hashiguchi A, Tian J, Komatsu S (2017) Proteomic contributions to medicinal plant research: from plant metabolism to pharmacological action. Proteomes 5(4):35. https://doi.org/10.3390/proteomes5040035
Hayut SF, Bessudo CM, Levy AA (2017) Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 8:15605. https://doi.org/10.1038/ncomms15605
He J, Giusti MM (2010) Anthocyanins: natural colorants with health-promoting properties. Annu Rev Food Sci Technol 1:163–187. https://doi.org/10.1146/annurev.food.080708.100754
He Y, Peng F, Deng C, **ong L, Huang Z, Zhang R, Liu M, Peng C (2018) Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. Sci Data 5(1):180274. https://doi.org/10.1038/sdata.2018.274
Heber D, Yip I, Ashley JM, Elashoff DA, Elashoff RM, Go VLW (1999) Cholesterol-lowering effects of a proprietary Chinese red-yeast-rice dietary supplement. Am J Clin Nutr 69(2):231–236. https://doi.org/10.1093/ajcn/69.2.231
Hidalgo D, Sanchez R, Lalaleo L, Bonfill M, Corchete P, Palazon J (2018) Biotechnological production of pharmaceuticals and biopharmaceuticals in plant cell and organ cultures. Curr Med Chem 25(30):3577–3596. https://doi.org/10.2174/0929867325666180309124317
Hoopes GM, Hamilton JP, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, Buell CR (2017) Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides. G3-Genes Genom Genet 8(2):385–391. https://doi.org/10.1534/g3.117.300331
Hou CC, Chen CH, Yang NS, Chen YP, Lo CP, Wang SY, Tien Y-J, Tsai P-W, Shyur L-F (2010) Comparative metabolomics approach coupled with cell-and gene-based assays for species classification and anti-inflammatory bioactivity validation of Echinacea plants. J Nutr Biochem 21(11):1045–1059. https://doi.org/10.1016/j.jnutbio.2009.08.010
Hu JC (2017) 4 Ways this revolutionary gene-editing tool could change the world. https://www.nbcnews.com/storyline/the-big-questions/4-ways-revolutionary-gene-editing-tool-could-change-world-n726371. Accessed 13 Dec 2020
Hua Q, Zhou Q, Gan S, Wu J, Chen C, Li J, Ye Y, Zhao J, Hu G, Qin Y (2016) Proteomic analysis of Hylocereus polyrhizus reveals metabolic pathway changes. Int J Mol Sci 17(10). https://doi.org/10.3390/ijms17101606
Huang L, Yang X, Sun P, Tong W, Hu S, Zhanjiang L (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 7(6). https://doi.org/10.1371/journal.pone.0038653
Hussain MS, Fareed S, Ansari S, Rahman MA, Ahmad IZ, Saeed M (2012) Current approaches towards production of secondary plant metabolites. J Pharm Bioallied Sci 4(1):10–20. https://doi.org/10.4103/0975-7406.92725
Hussein RA, El-Anssary AA (2018) Plants secondary metabolites: the key drivers of the pharmacological actions of medicinal plants. In: Herbal medicine. IntechOpen, London
Iaffaldano B, Zhang Y, Cornish K (2016) CRISPR/Cas9 genome editing of rubber producing dandelion Taraxacum kok-saghyz using Agrobacterium rhizogenes without selection. Ind Crop Prod 89:356–362. https://doi.org/10.1016/j.indcrop.2016.05.029
Ishida M, Hara M, Fukino N, Kakizaki T, Morimitsu Y (2014) Glucosinolate metabolism, functionality and breeding for the improvement of Brassicaceae vegetables. Breed Sci 64(1):48–59. https://doi.org/10.1270/jsbbs.64.48
Jacobs DI, Gaspari M, van der Greef J, van der Heijden R, Verpoorte R (2005) Proteome analysis of the medicinal plant Catharanthus roseus. Planta 221:690–704. https://doi.org/10.1007/s00425-004-1474-4
Jamshidi-Kia F, Lorigooini Z, Amini-Khoei H (2018) Medicinal plants: past history and future perspective. J Herb Med Pharmacol 7(1):1–7. https://doi.org/10.15171/jhp.2018.01
Jia H, Wang N (2014) Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 9:e93806. https://doi.org/10.1371/journal.pone.0093806
Jiao R, Gao C (2016) The CRISPR/Cas9 genome editing revolution. JGG 43(5):227–228. https://doi.org/10.1016/j.jgg.2016.05.004
** H, Yu H, Wang H, Zhang J (2020) Comparative proteomic analysis of Dipsacus asperoides roots from different habitats in China. Molecules 25. https://doi.org/10.3390/molecules25163605
Joung JK, Sander JD (2012) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14(1):49–55. https://doi.org/10.1038/nrm3486
Kai G, Xu H, Zhou C, Liao P, **ao J, Luo X, You L, Zhang L (2011) Metabolic engineering tanshinone biosynthetic pathway in Salvia miltiorrhiza hairy root cultures. Metab Eng 13(3):319–327. https://doi.org/10.1016/j.ymben.2011.02.003
Kang M, Wu H, Yang Q, Huang L, Hu Q, Ma T, Li Z, Liu J (2020) A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine. Hortic Res 7:18. https://doi.org/10.1038/s41438-020-0240-5
Karpievitch YV, Polpitiya AD, Anderson GA, Smith RD, Dabney AR (2010) Liquid chromatography mass spectrometry-based proteomics: biological and technological aspects. Ann Appl Stat 4(4):1797–1823. https://doi.org/10.1214/10-aoas341
Karuppusamy S (2009) A review on trends in production of secondary metabolites from higher plants by in vitro tissue, organ and cell cultures. J Med Plant Res 3(13):1222–1239. https://doi.org/10.5897/JMPR.9000026
Kaur R, Kapoor K, Kaur H (2011) Plants as a source of anticancer agents. J Nat Prod Plant Resour 1(1):119–124. https://doi.org/10.1016/j.jep.2005.05.011
Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O’Connor SE (2015) Genome-guided investigation of plant natural product biosynthesis. Plant J 82:680–692. https://doi.org/10.1111/tpj.12827
Kennedy DO, Wightman EL, Okello EJ (2010) Chapter 27. Medicinal plants, phytochemicals and Alzheimer’s disease. In: Martinez A (ed) Emerging drugs and targets for Alzheimer’s disease, vol 2. RSC Publishing, Cambridge, pp 269–290
Kerckhoffs DAJM, Brouns F, Hornstra G, Mensink RP (2002) Effects on the human serum lipoprotein profile of β-glucan, soy protein and isoflavones, plant sterols and stanols, garlic and tocotrienols. J Nutr 132(9):2494–2505. https://doi.org/10.1093/jn/132.9.2494
Keurentjes JJB, Fu J, de Vos CHR, Lommen A, Hall RD, Bino RJ, Koornneef M (2006) The genetics of plant metabolism. Nat Genet 38(7):842–849. https://doi.org/10.1038/ng1815
Key S, Ma JK-C, Drake PM (2008) Genetically modified plants and human health. J R Soc Med 101(6):290–298. https://doi.org/10.1258/jrsm.2008.070372
Khan SH (2019) Genome-editing technologies: concept, pros, and cons of various genome-editing techniques and bioethical concerns for clinical application. Mol Ther Nucleic Acids 16:326–334. https://doi.org/10.1016/j.omtn.2019.02.027
Khezerluo M, Hosseini B, Amiri J (2018) Sodium nitroprusside stimulated production of tropane alkaloids and antioxidant enzymes activity in hairy root culture of Hyoscyamus reticulatus L. Acta Biol Hung 69(4):437–448. https://doi.org/10.1556/018.69.2018.4.6
Khoomrung S, Wanichthanarak K, Nookaew I, Thamsermsang O, Seubnooch P, Laohapand T, Akarasereenont P (2017) Metabolomics and integrative omics for the development of Thai traditional medicine. Front Pharmacol 8. https://doi.org/10.3389/fphar.2017.00474
Kim YS, Hahn EJ, Murthy HN, Paek KY (2004) Adventitious root growth and ginsenoside accumulation in Panax ginseng cultures as affected by methyl jasmonate. Biotechnol Lett 26:1619–1622. https://doi.org/10.1007/s10529-004-3183-2
Kim OT, Kim SH, Ohyama K, Muranaka T, Choi YE, Lee HY, Kim MY, Hwang B (2010a) Upregulation of phytosterol and triterpene biosynthesis in Centella asiatica hairy roots overexpressed ginseng farnesyl diphosphate synthase. Plant Cell Rep 29:403–411
Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH (2010b) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. PNAS 107(51):22032–22037. https://doi.org/10.1073/pnas.1009526107
Kim MJ, Nelson W, Soderlund CA, Gang DR (2013a) Next generation sequencing-based transcriptional profiling of sacred lotus ‘china antique’. Trop Plant Biol 6:161–179
Kim Y-K, Kim JK, Kim YB, Lee S, Kim S-U, Park SU (2013b) Enhanced accumulation of phytosterol and triterpene in hairy root cultures of Platycodon grandiflorum by overexpression of Panax ginseng 3-hydroxy-3-methylglutaryl-coenzyme a reductase. J Agric Food Chem 61(8):1928–1934. https://doi.org/10.1021/jf304911t
Kim S, Park M, Yeom S-I, Kim Y-M, Lee JM, Lee H-A, Seo E, Choi J, Cheong K, Kim K-T, Jung K, Lee G-W, Oh S-K, Bae C, Kim S-B, Lee H-Y, Kim S-Y, Kim M-S, Kang B-C, Jo YD, Yang H-B, Jeong H-J, Kang W-H, Kwon J-K, Shin C, Lim JY, Park JH, Huh JH, Kim J-S, Kim B-D, Cohen O, Paran I, Suh MC, Lee SB, Kim Y-K, Shin Y, Noh S-J, Park J, Seo YS, Kwon S-Y, Kim HA, Park JM, Kim H-J, Choi S-B, Bosland PW, Reeves G, Jo S-H, Lee B-W, Cho H-T, Choi H-S, Lee M-S, Yu Y, Do Choi Y, Park B-S, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai H-S, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee S-J, Kim RW, Choi I-Y, Choi B-S, Lim J-S, Lee Y-H, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46(3):270–278. https://doi.org/10.1038/ng.2877
Kim SW, Gupta R, Lee SH, Min CW, Agrawal GK, Rakwal R, Kim JB, Jo IH, Park S-Y, Kim JK, Kim Y-C, Bang KH, Kim ST (2016) An integrated biochemical, proteomics, and metabolomics approach for supporting medicinal value of Panax ginseng fruits. Front Plant Sci 7. https://doi.org/10.3389/fpls.2016.00994
Kim JA, Roy NS, Lee I, Choi AY, Choi BS, Yu YS, Park NI, Park KC, Kim S, Yang H, Choi YY (2019) Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach. Genomics 111(4):973–979. https://doi.org/10.1016/j.ygeno.2018.06.004
Kobayashi Y, Fukui H, Tabata M (1991) Effect of carbon dioxide and ethylene on berberine production and cell browning in Thalictrum minus cell cultures. Plant Cell Rep 9:496–499. https://doi.org/10.1007/BF00232104
Kolker E, Higdon R, Hogan JM (2006) Protein identification and expression analysis using mass spectrometry. Trends Microbiol 14(5):229–235. https://doi.org/10.1016/j.tim.2006.03.005
Kortbeek RWJ, Xu J, Ramirez A, Spyropoulou E, Diergaarde P, Otten-Bruggeman I, Bleeker PM (2016) Engineering of tomato glandular trichomes for the production of specialized metabolites. In: Methods in enzymology. Academic Press, San Diego, CA, pp 305–331
Kotwal S, Kaul S, Sharma P, Gupta M, Shankar R, Jain M, Dhar MK (2016) De novo transcriptome analysis of medicinally important Plantago ovata using RNAseq. PLoS One 11(3). https://doi.org/10.1371/journal.pone.0150273
Kumar D, Bansal G, Narang A, Basak T, Abbas T, Dash D (2016) Integrating transcriptome and proteome profiling: strategies and applications. Proteomics 16(19):2533–2544. https://doi.org/10.1002/pmic.201600140
Kurien BT, Scofield RH (2012) Extraction of proteins from gels: a brief review. In: Protein electrophoresis. Springer, Berlin, pp 403–405
Kurup VM, Thomas J (2020) Edible vaccines: promises and challenges. Mol Biotechnol 62(2):79–90. https://doi.org/10.1007/s12033-019-00222-1
Kusano M, Tabuchi M, Fukushima A, Funayama K, Diaz C, Kobayashi M, Hayashi N, Tsuchiya YN, Takahashi H, Kamata A, Yamaya T, Saito K (2011) Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. Plant J 66:456–466. https://doi.org/10.1111/j.1365-313X.2011.04506.x
Kyoto Encyclopedia of Genes and Genomes (2006) KEGG pathway database. https://www.genome.jp/kegg/pathway.html. Accessed 6 Dec 2020
Labant MA (2020) Redesigning the global food supply. https://www.genengnews.com/insights/redesigning-the-global-food-supply/. Accessed 13 Dec 2020
Lee YS, Park HS, Lee DK, Jayakodi M, Kim NH, Koo HJ, Lee SC, Kim YJ, Kwon SW, Yang TJ (2017) Integrated transcriptomic and metabolomic analysis of five Panax ginseng cultivars reveals the dynamics of ginsenoside biosynthesis. Front Plant Sci 8. https://doi.org/10.3389/fpls.2017.01048
Leete E (1980) Biosynthesis of cocaine and cuscohygrine in Erythroxylon coca. J Chem Soc Chem Commun 22(3). https://doi.org/10.1039/c39800001170
Leicach SR, Chludil SD (2014) Plant secondary metabolites: structure–activity relationships in human health prevention and treatment of common diseases. Stud Nat Prod Chem 42:267–304. https://doi.org/10.1016/B978-0-444-63281-4.00009-4
Li Y, Luo H-M, Sun C, Song J-Y, Sun Y-Z, Wu Q, Wang N, Yao H, Steinmetz A, Chen S-L (2010) EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genomics 11(1):268. https://doi.org/10.1186/1471-2164-11-268
Li B, Cui G, Shen G, Zhan Z, Huang L, Chen J, Qi X (2017b) Targeted mutagenesis in the medicinal plant Salvia miltiorrhiza. Sci Rep 7(1):43320. https://doi.org/10.1038/srep43320
Li Q, Ding G, Li B, Guo SX (2017a) Transcriptome Analysis of genes involved in dendrobine biosynthesis in Dendrobium nobile Lindl. infected with mycorrhizal fungus MF23 (Mycena sp.). Sci Rep 7(1). https://doi.org/10.1038/s41598-017-00445-9
Li T, Wang Y-H, Liu J-X, Feng K, Xu Z-S, **ong A-S (2019) Advances in genomic, transcriptomic, proteomic, and metabolomic approaches to study biotic stress in fruit crops. Crit Rev Biotechnol 39:680–692. https://doi.org/10.1080/07388551.2019.1608153
Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X (2020) Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther 5(1). https://doi.org/10.1038/s41392-019-0089-y
Liu M-J, Zhao J, Cai Q-L, Liu G-C, Wang J-R, Zhao Z-H, Liu P, Dai L, Yan G, Wang W-J, Li X-S, Chen Y, Sun Y-D, Liu Z-G, Lin M-J, **ao J, Chen Y-Y, Li X-F, Wu B, Ma Y, Jian J-B, Yang W, Yuan Z, Sun X-C, Wei Y-L, Yu L-L, Zhang C, Liao S-G, He R-J, Guang X-M, Wang Z, Zhang Y-Y, Luo L-H (2014) The complex jujube genome provides insights into fruit tree biology. Nat Commun 5(1):5315. https://doi.org/10.1038/ncomms6315
Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B (2017) Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 18(1). https://doi.org/10.1186/s12864-017-3869-1
Liu Y, Tang Q, Cheng P, Zhu M, Zhang H, Liu J, Liu Z (2019) Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans. APSB 10(2):374–382. https://doi.org/10.1016/j.apsb.2019.08.004
Liu P, Luo J, Zheng Q, Chen Q, Zhai N, Xu S, Xu Y, ** L, Xu G, Lu X, Xu G, Wang G, Shao J, Xu HM, Cao P, Zhou H, Wang X (2020) Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco. DNA Res 27(2). https://doi.org/10.1093/dnares/dsaa006
Livingston SJ, Quilichini TD, Booth JK, Wong DCJ, Rensing KH, Laflamme-Yonkman J, Samuels AL (2019) Cannabis glandular trichomes alter morphology and metabolite content during flower maturation. Plant J 101(1):37–56. https://doi.org/10.1111/tpj.14516
Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (2000) Molecular biology of the cell, 4th edn. W.H. Freeman, New York
Loewe L, Hill WG (2010) The population genetics of mutations: good, bad and indifferent. Philos Trans R Soc Lond Ser B Biol Sci 365(1544):1153–1167. https://doi.org/10.1098/rstb.2009.0317
Loureiro A, da Silva G (2019) CRISPR-Cas: converting a bacterial defence mechanism into state-of-the-art genetic manipulation tool. Antibiotics 8(1):18. https://doi.org/10.3390/antibiotics8010018
Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13(5):e1005457. https://doi.org/10.1371/journal.pcbi.1005457
Ma D, Hu Y, Yang C, Liu B, Fang L, Wan Q, Liang W, Mei G, Wang L, Wang H, Ding L, Dong C, Pan M, Chen J, Wang S, Chen S, Cai C, Zhu X, Guan X, Zhou B, Zhu S, Wang J, Guo W, Chen X, Zhang T (2016a) Genetic basis for glandular trichome formation in cotton. Nat Commun 7:10456. https://doi.org/10.1038/ncomms10456
Ma R, Sun L, Chen X, Mei B, Chang G, Wang M, Zhao D (2016b) Proteomic analyses provide novel insights into plant growth and ginsenoside biosynthesis in forest cultivated Panax ginseng (F. Ginseng). Front Plant Sci 7. https://doi.org/10.3389/fpls.2016.00001
Maeder ML, Gersbach CA (2016) Genome-editing technologies for gene and cell therapy. Mol Ther 24(3):430–446. https://doi.org/10.1038/mt.2016.10
Maghari BM, Ardekani AM (2011) Genetically modified foods and social concerns. Avicenna J Med Biotechnol 3(3):109–117
Magnotta M, Murata J, Chen J, De Luca V (2007) Expression of deacetylvindoline-4-O-acetyltransferase in Catharanthus roseus hairy roots. Phytochemistry 68(14):1922–1931. https://doi.org/10.1016/j.phytochem.2007.04.037
Manzoni C, Kia DA, Vandrovcova J, Hardy J, Wood NW, Lewis PA, Ferrari R (2018) Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. Brief Bioinform 19(2):286–302. https://doi.org/10.1093/bib/bbw114
Mazzafera P, Crozier A, Magalhães AC (1991) Caffeine metabolism in Coffea arabica and other species of coffee. Phytochemistry 30(12):3913–3916. https://doi.org/10.1016/0031-9422(91)83433-l
McGhie TK, Rowan DD (2011) Metabolomics for measuring phytochemicals, and assessing human and animal responses to phytochemicals, in food science. Mol Nutr Food Res 56(1):147–158. https://doi.org/10.1002/mnfr.201100545
Medicinal Plant Genomics (2017) Medicinal plant genomics resource. http://medicinalplantgenomics.msu.edu/index.shtml. Accessed 25 Jan 2020
Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS (2017) Abiotic stress responses and microbe-mediated mitigation in plants: the omics strategies. Front Plant Sci 8. https://doi.org/10.3389/fpls.2017.00172
Mehta RH, Ponnuchamy M, Kumar J (2017) Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomics 17(1):1–25. https://doi.org/10.1007/s10142-016-0523-y
Menz J, Modrzejewski D, Hartung F, Wilhelm R, Sprink T (2020) Genome edited crops touch the market: a view on the global development and regulatory environment. Front Plant Sci 11. https://doi.org/10.3389/fpls.2020.586027
Metje-Sprink J, Menz J, Modrzejewski D, Sprink T (2019) DNA-free genome editing: past, present and future. Front Plant Sci 9. https://doi.org/10.3389/fpls.2018.01957
Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Qu L-J (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23(10):1233–1236. https://doi.org/10.1038/cr.2013.123
Mishra RR (2019) Adoption of genetically modified crops can ensure food security in India. Natl Acad Sci Lett 43:213–221. https://doi.org/10.1007/s40009-019-00829-7
Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, Uchiyama H, Muranaka T, Saito K (2016) Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J 89(2):181–194. https://doi.org/10.1111/tpj.13385
Montecillo JAV, Chu LL, Bae H (2020) CRISPR-Cas9 system for plant genome editing: current approaches and emerging developments. Agronomy 10(7):1033. https://doi.org/10.3390/agronomy10071033
Monti M, Orrù S, Pagnozzi D, Pucci P (2005) Functional proteomics. Clin Chim Acta 357(2):140–150. https://doi.org/10.1016/j.cccn.2005.03.019
Monti M, Cozzolino M, Cozzolino F, Tedesco R, Pucci P (2007) Functional proteomics: protein-protein interactions in vivo. Ital J Biochem 56(4):310–314
Muranaka T, Saito K (2013) Phytochemical genomics on the way. Plant Cell Physiol 54(5):645–646. https://doi.org/10.1093/pcp/pct058
Murch SJ, Rupasinghe HPV, Goodenowe D, Saxena PK (2004) A metabolomic analysis of medicinal diversity in Huang-qin (Scutellaria baicalensis Georgi) genotypes: discovery of novel compounds. Plant Cell Rep 23:419–425. https://doi.org/10.1007/s00299-004-0862-3
Nadiya F, Anjali N, Thomas J, Gangaprasad A, Sabu (2017) Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom). Genom Data 11:102–103. doi: https://doi.org/10.1016/j.gdata.2016.12.013
Nair AJ, Sudhakaran PR, Rao JM, Ramakrishna SV (1992) Berberine synthesis by callus and cell suspension cultures of Coscinium fenestratum. Plant Cell Tissue Organ 29:7–10. https://doi.org/10.1007/BF00036139
Najafov A, Hoxhaj G (2017) Introduction. In: Western blotting guru. Academic Press, London, pp 1–3
Nakabayashi R, Saito K (2015) Integrated metabolomics for abiotic stress responses in plants. Curr Opin Plant Biol 24:10–16. https://doi.org/10.1016/j.pbi.2015.01.003
Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, Yamamoto T, Toki S, Endo M (2017) CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One 12(5):e0177966. https://doi.org/10.1371/journal.pone.0177966
Nakase I, Lai H, Singh NP, Sasaki T (2008) Anticancer properties of artemisinin derivatives and their targeted delivery by transferrin conjugation. Int J Pharm 354:28–33. https://doi.org/10.1016/j.ijpharm.2007.09.003
Namukobe J, Kasenene JM, Kiremire BT, Byamukama R, Kamatenesi-Mugisha M, Krief S, Dumontet V, Kabasa JD (2011) Traditional plants used for medicinal purposes by local communities around the Northern sector of Kibale National Park, Uganda. J Ethnopharmacol 136(1):236–245. https://doi.org/10.1016/j.jep.2011.04.044
Narnoliya LK, Kaushal G, Singh SP (2019) Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium. FEBS Lett 593(16):2235–2249. https://doi.org/10.1002/1873-3468.13493
Nawrot R, Zauber H, Schulze WX (2014) Global proteomic analysis of Chelidonium majus and Corydalis cava (Papaveraceae) extracts revealed similar defense-related protein compositions. Fitoterapia 94:77–87. https://doi.org/10.1016/j.fitote.2014.01.015
Ncube B, Van Staden J (2015) Tilting plant metabolism for improved metabolite biosynthesis and enhanced human benefit. Molecules 20(7):12698–12731. https://doi.org/10.3390/molecules200712698
Nielsen E, Temporiti MEE, Cella R (2019) Improvement of phytochemical production by plant cells and organ culture and by genetic engineering. Plant Cell Rep 38(10):1199–1215. https://doi.org/10.1007/s00299-019-02415-z
Okada T, Takahashi H, Suzuki Y, Sugano S, Noji M, Kenmoku H, Toyota M, Kanaya S, Kawahara N, Asakawa Y, Sekita S (2016) Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing. Genom Data 10:4–11. https://doi.org/10.1016/j.gdata.2016.08.003
Okazaki Y, Saito K (2012) Recent advances of metabolomics in plant biotechnology. Plant Biotechnol Rep 6(1):1–15. https://doi.org/10.1007/s11816-011-0191-2
Oksman-Caldentey K-M, Inzé D (2004) Plant cell factories in the post-genomic era: new ways to produce designer secondary metabolites. Trends Plant Sci 9(9):433–440. https://doi.org/10.1016/j.tplants.2004.07.006
Ou L, Liu Z, Zhang Z, Wei G, Zhang Y, Kang L, Yang B, Yang S, Lv J, Liu Y, Chen W, Dai X, Li X, Zhou S, Ma Y, Zou X (2017) Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.). Plant Growth Regul 83(1):141–156. https://doi.org/10.1007/s10725-017-0290-3
Palazón J, Cusidó RM, Bonfill M, Mallol A, Moyano E, Morales C, Piñol MT (2003) Elicitation of different Panax ginseng transformed root phenotypes for an improved ginsenoside production. Plant Physiol Biochem 41:1019–1025. https://doi.org/10.1016/j.plaphy.2003.09.002
Pan C, Ye L, Qin L, Liu X, He Y, Wang J, Chen L, Lu G (2016) CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6(1):24765. https://doi.org/10.1038/srep24765
Pandit S, Kumar M, Ponnusankar S, Pal BC, Mukherjee PK (2010) RP-HPLC-DAD for simultaneous estimation of mahanine and mahanimbine in Murraya koenigii. Biomed Chromatogr 25:959–962. https://doi.org/10.1002/bmc.1561
Pasquali M, Serchi T, Planchon S, Renaut J (2017) 2D-DIGE in proteomics. In: Kaufmann M, Klinger C, Savelsbergh A (eds) Functional genomics. Springer, Berlin, pp 245–254
Pathak S, Agarwal AV, Agarwal P, Trivedi PK (2019) Secondary metabolite pathways in medicinal plants: approaches in reconstruction and analysis. In: Molecular approaches in plant biology and environmental challenges. Springer, Singapore, pp 339–364
Patra S, Andrew AA (2015) Human, social, and environmental impacts of human genetic engineering. J Biomed Sci 4:2. https://doi.org/10.4172/2254-609X.100014
Payyappallimana U (2010) Role of traditional medicine in primary health care: an overview of perspectives and challenging. Yokohama J Soc Sci 14(6):723–743
Petolino JF (2015) Genome editing in plants via designed zinc finger nucleases. In Vitro Cell Dev Biol Plant 51(1). https://doi.org/10.1007/s11627-015-9663-3
Philip VJ, Nainar AZ (1986) Clonal propagation of Vanilla planifolia (Salisb.) Ames using tissue culture. J Plant Physiol 122:211–215. https://doi.org/10.1016/S0176-1617(86)80119-5
Phillips T (2008) Genetically modified organisms (GMOs): Transgenic crops and recombinant DNA technology. Nat Educ 1(1):213
Phillipson JD (1994) Natural products as drugs. Trans R Soc Trop Med Hyg 88:17–19. https://doi.org/10.1016/0035-9203(94)90464-2
Piasecka A, Kachlicki P, Stobiecki M (2019) Analytical methods for detection of plant metabolomes changes in response to biotic and abiotic stresses. Int J Mol Sci 20(2):379. https://doi.org/10.3390/ijms20020379
Plotkin MJ, Balick MJ (1984) Medicinal uses of South American palms. J Ethnopharmacol 10(2):157–179. https://doi.org/10.1016/0378-8741(84)90001-1
Ponomarenko EA, Poverennaya EV, Ilgisonis EV, Pyatnitskiy MA, Kopylov AT, Zgoda VG, Lisitsa AV, Archakov AI (2016) The size of the human proteome: the width and depth. Int J Anal Chem 2016:1–6. https://doi.org/10.1155/2016/7436849
Pu X, Li Z, Tian Y, Gao R, Hao L, Hu Y, He C, Sun W, Xu M, Peters RJ, Van de Peer Y, Xu Z, Song J (2020) The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. New Phytol 227(3):930–943. https://doi.org/10.1111/nph.16552
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, Gonzalez-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernandez S, Leyva-Gonzalez MA, **ong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, Zhang Z (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A 111(14):5135–5140. https://doi.org/10.1073/pnas.1400975111
Quiroz HC (2002) Plant genomics: an overview. Biol Res 35(3–4):385–399. https://doi.org/10.4067/S0716-97602002000300013
Raharjo TJ, Widjaja I, Roytrakul S, Verpoorte R (2004) Comparative proteomics of Cannabis sativa plant tissues. J Biomol Technol 15:97–106
Rai A, Nakamura M, Takahashi H, Suzuki H, Saito K, Yamazaki M (2016) High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites. Plant Cell Rep 35:2091–2111. https://doi.org/10.1007/s00299-016-2021-z
Rai A, Saito K, Yamazaki M (2017) Integrated omics analysis of specialized metabolism in medicinal plants. Plant J 90:764–787. https://doi.org/10.1111/tpj.13485
Raman R (2017) The impact of Genetically Modified (GM) crops in modern agriculture: a review. GM Crops Food 8:195–208. https://doi.org/10.1080/21645698.2017.1413522
Ramirez-Estrada K, Vidal-Limon H, Hidalgo D, Moyano E, Golinowski M, Cusido RM, Palazon J (2016) Elicitation, an effective strategy for the biotechnological production of bioactive high-added value compounds in plant cell factories. Molecules 21(182). https://doi.org/10.3390/molecules21020182
Rao SR, Ravishankar GA (2002) Plant cell cultures: chemical factories of secondary metabolites. Biotechnol Adv 20:101–153. https://doi.org/10.1016/S0734-9750(02)00007-1
Rates SMK (2001) Plants as source of drugs. Toxicon 39(5):603–613. https://doi.org/10.1016/s0041-0101(00)00154-9
Rehman S, Ul Rehman I, Jan B, Rashid I, Ah Reshi Z, Ganie AH (2020) Genome editing: applications for medicinal and aromatic plants. Med Aromatic Plants:119–144. https://doi.org/10.1016/b978-0-12-819590-1.00006-9
Robins RJ, Rhodes MJC (1986) The stimulation of anthraquinone production by Cinchona ledgeriana cultures with polymeric adsorbents. Appl Microbiol Biotechnol 24:35–41. https://doi.org/10.1007/BF00266282
Romagnoli LG, Knorr D (1988) Effects of ferulic acid treatment on growth and flavor development of cultured Vanilla planifolia cells. Food Biotechnol 2(1):93–104. https://doi.org/10.1080/08905438809549678
Saito K (2013) Phytochemical genomics—a new trend. Curr Opin Plant Biol 16(3):373–380. https://doi.org/10.1016/j.pbi.2013.04.001
Saito K, Matsuda F (2010) Metabolomics for functional genomics, systems biology, and biotechnology. Annu Rev Plant Biol 61(1):463–489. https://doi.org/10.1146/annurev.arplant.043008.092035
Sanchez-Pujante PJ, Borja-Martinez M, Pedreno MA, Almagro L (2017) Biosynthesis and bioactivity of glucosinolates and their production in plant in vitro cultures. Planta 246(1). https://doi.org/10.1007/s00425-017-2705-9
Sangwan NS, Tripathi S, Srivastava Y, Mishra B, Pandey N (2017) Phytochemical genomics of ashwagandha. In: Kaul S, Wadhwa R (eds) Science of ashwagandha: preventive and therapeutic potentials. Springer, Cham
Saraswathy N, Ramalingam P (2011) 10: Introduction to proteomics. In: Concepts and techniques in genomics and proteomics. Woodhead Publishing Series, Oxford, pp 147–158
Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, Sakurai T, Saito K, Hirai MY (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol 50(1):37–47. https://doi.org/10.1093/pcp/pcn183
Saxena M, Saxena J, Nema R, Singh D, Gupta A (2013) Phytochemistry of medicinal plants. J Pharmacogn Phytochem 1(6):168–182
Scartezzini P, Speroni E (2000) Review on some plants of Indian traditional medicine with antioxidant activity. J Ethnopharmacol 71(1–2):23–43. https://doi.org/10.1016/s0378-8741(00)00213-0
Schachtsiek J, Warzecha H, Kayser O, Stehle F (2018) Current perspectives on biotechnological cannabinoid production in plants. Planta Med 84(4):214–220. https://doi.org/10.1055/s-0043-125087
Schaeffer SM, Nakata PA (2015) CRISPR/Cas9-mediated genome editing and gene replacement in plants: transitioning from lab to field. Plant Sci 240:130–142. https://doi.org/10.1016/j.plantsci.2015.09.011
Schuurink R, Tissier A (2019) Glandular trichomes: micro-organs with model status? New Phytol. https://doi.org/10.1111/nph.16283
Seca AML, Pinto DCGA (2019) Biological potential and medical use of secondary metabolites. Medicines 6(2):66. https://doi.org/10.3390/medicines6020066
Segovia FJ, Luengo E, Corral-Perez JJ, Raso J, Almajano MP (2014) Improvements in the aqueous extraction of polyphenols from borage (Borago officinalis L.) leaves by pulsed electric fields: pulsed electric fields (PEF) applications. Ind Crop Prod 65:390–396. https://doi.org/10.1016/j.indcrop.2014.11.010
Segura B (2003) Red yeast rice: an easy way to lower cholesterol. Nutr Bytes 9(1). https://escholarship.org/uc/item/8hc9q39b
Seligman LM (2002) Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res 30(17):3870–3879. https://doi.org/10.1093/nar/gkf495
Seymour V (2016) The human–nature relationship and its impact on health: a critical review. Front Public Health 4:260. https://doi.org/10.3389/fpubh.2016.00260
Shafiq S, Li J, Sun Q (2016) Functions of plants long non-coding RNAs. Biochim Biophys Acta 1859(1):155–162. https://doi.org/10.1016/j.bbagrm.2015.06.009
Shahin A, van Kaauwen M, Esselink D, Bargsten JW, van Tuyl JM, Visser RGF, Arens P (2012) Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa. BMC Genomics 13(1):640. https://doi.org/10.1186/1471-2164-13-640
Sharafi A, Hashemi Sohi H, Mousavi A, Azadi P, Dehsara B, Hosseini Khalifani B (2013) Enhanced morphinan alkaloid production in hairy root cultures of Papaver bracteatum by over-expression of salutaridinol 7-o-acetyltransferase gene via Agrobacterium rhizogenes mediated transformation. World J Microbiol Biotechnol 29(11):2125–2131. https://doi.org/10.1007/s11274-013-1377-2
Sharma V, Sarkar IN (2012) Bioinformatics opportunities for identification and study of medicinal plants. Brief Bioinformatics 14(2):238–250. https://doi.org/10.1093/bib/bbs021
Shen C, Guo H, Chen H, Shi Y, Meng Y, Lu J, Feng S, Wang H (2017) Identification and analysis of genes associated with the synthesis of bioactive constituents in Dendrobium officinale using RNA-Seq. Sci Rep 7(1). https://doi.org/10.1038/s41598-017-00292-8
Shen Q, Zhang L, Liao Z, Wang S, Yan T, Shi P, Liu M, Fu X, Pan Q, Wang Y, Lv Z, Lu X, Zhang F, Jiang W, Ma Y, Chen M, Hao X, Li L, Tang Y, Lv G, Zhou Y, Sun X, Brodelius PE, Rose JKC, Tang K (2018) The genome of Artemisia annua provides insight into the evolution of Asteraceae family and artemisinin biosynthesis. Mol Plant 11(6):776–788. https://doi.org/10.1016/j.molp.2018.03.015
Sheth BP, Thaker VS (2014) Plant systems biology: insights, advances and challenges. Planta 240(1):33–54. https://doi.org/10.1007/s00425-014-2059-5
Shew AM, Nalley LL, Snell HA, Nayga RM Jr, Dixon BL (2018) CRISPR versus GMOs: public acceptance and valuation. Glob Food Secur 19:71–80. https://doi.org/10.1016/j.gfs.2018.10.005
Shinbo Y, Nakamura Y, Altaf-Ul-Amin M, Asahi H, Kurokawa K, Arita M, Saito K, Ohta D, Shibata D, Kanaya S (2006) KNApSAcK: a comprehensive species-metabolite relationship database. In: Saito K, Dixon RA, Willmitzer L (eds) Plant metabolomics. Biotechnology in agriculture and forestry, vol 57. Springer, Berlin, pp 165–181
Shiraishi A, Murata J, Matsumoto E, Matsubara S, Ono E, Satake H, Jain M (2016) De novo transcriptomes of Forsythia koreana using a novel assembly method: insight into tissue- and species specific expression of lignan biosynthesis-related gene. PLoS One 11(10):e0164805. https://doi.org/10.1371/journal.pone.0164805
Shitan N (2016) Secondary metabolites in plants: transport and self tolerance mechanisms. Biosci Biotechnol Biochem 80(7):1283–1293. https://doi.org/10.1080/09168451.2016.1151344
Sikora P, Chawade A, Larsson M, Olsson J, Olsson O (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genomics 2011:1–13. https://doi.org/10.1155/2011/314829
Soda N, Wallace S, Karan R (2015) Omics study for abiotic stress responses in plants. APAR 2(1):28–34. https://doi.org/10.15406/apar.2015.02.00037
Soliman GA (2019) Dietary fiber, atherosclerosis, and cardiovascular disease. Nutrients 11(5):1155. https://doi.org/10.3390/nu11051155
Song Z, Lin C, **ng P, Fen Y, ** H, Zhou C, Gu YQ, Wang J, Li X (2020) A high-quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes. TPG 13(3). https://doi.org/10.1002/tpg2.20041
Srivastava A, George J, Karuturi RKM (2019) Transcriptome analysis. In: Encyclopedia of bioinformatics and computational biology, vol 3. Elsevier, Amsterdam, pp 792–805
Staba EJ, Chung AC (1981) Quinine and quinidine production by Cinchona leaf, root and unorganized cultures. Phytochemistry 20(11):2495–2498. https://doi.org/10.1016/0031-9422(81)83079-8
Stanojković J, Todorović S, Pećinar I, Lević S, Ćalić S, Janošević D (2020) Leaf glandular trichomes of micropropagated Inula britannica—effect of sucrose on trichome density, distribution and chemical profile. Ind Crop Prod 160:113101. https://doi.org/10.1016/j.indcrop.2020.113101
Stoddard BL (2006) Homing endonuclease structure and function. Q Rev Biophys 38(1):49–95. https://doi.org/10.1017/s0033583505004063
Su T, Liu F, Gu P, ** H, Chang Y, Wang Q, Liang Q, Qi Q (2016) A CRISPR-Cas9 assisted non-homologous end-joining strategy for one-step engineering of bacterial genome. Sci Rep 6:37895. https://doi.org/10.1038/srep37895
Sun Y, Xun K, Wang Y, Chen X (2009) A systematic review of the anticancer properties of berberine, a natural product from Chinese herbs. Anti-Cancer Drugs 20:757–769. https://doi.org/10.1097/CAD.0b013e328330d95b
Sun W, Leng L, Yin Q, Xu M, Huang M, Xu Z, Zhang Y, Yao H, Wang C, **ong C, Chen S, Jiang C, **e N, Zheng X, Wang Y, Song C, Peters RJ, Chen S (2019) The genome of the medicinal plant Andrographis paniculata provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide. Plant J 97(5):841–857. https://doi.org/10.1111/tpj.14162
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Seligman LM (2004) Isolation and characterization of new homing endonuclease specificities at individual target site positions. J Mol Biol 342(1):31–41. https://doi.org/10.1016/j.jmb.2004.07.031
Takahashi H, Hirai A, Shojo M, Matsuda K, Parvin AK, Asahi H, Nakamura K, Altaf-Ul-Amin M, Kanaya S (2011) Species-metabolite relation database KNApSAcK and its multifaceted retrieval system, KNApSAcK family. Gen Appl Syst Toxicol. https://doi.org/10.1002/9780470744307.gat218
Takanashi K, Nakagawa Y, Aburaya S, Kaminade K, Aoki W, Saida-Munakata Y, Sugiyama A, Ueda M, Yazaki K (2018) Comparative proteomic analysis of Lithospermum erythrorhizon reveals regulation of a variety of metabolic enzymes leading to comprehensive understanding of the shikonin biosynthetic pathway. Plant Cell Physiol 60(1):19–28. https://doi.org/10.1093/pcp/pcy183
Takeuchi R, Choi M, Stoddard BL (2014) Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. PNAS 111(11):4061–4066. https://doi.org/10.1073/pnas.1321030111
Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SAM, Sung YY, Van de Peer Y, Sorgeloos P, Danish-Daniel M (2019) Applications of Next-Generation Sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies: a short review. Evol Bioinforma 15:117693431989228. https://doi.org/10.1177/1176934319892284
Tang Q, Ma XJ, Mo CM, Wilson IW, Song C, Zhao H, Yang Y, Fu W, Qiu D (2011) An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics 12. https://doi.org/10.1186/1471-2164-12-343
The European Bioinformatics Institute (EMBL-EBI). What is genomics? https://www.ebi.ac.uk/. Accessed 10 Dec 2020
The Nobel Prize in Chemistry (2020) NobelPrize.org. https://www.nobelprize.org/prizes/chemistry/2020/press-release/. Accessed 13 Dec 2020
Thompson SD, Prahalad S, Colbert RA (2016) Integrative genomics. In: Textbook of pediatric rheumatology, 7th edn. Elsevier, Amsterdam, pp 43–53.e3
Tian L (2015) Using hairy roots for production of valuable secondary metabolites. Adv Biochem Eng Biotechnol 149:275–324. https://doi.org/10.1007/10_2014_298
Tian H, Xu X, Zhang F, Wang Y, Guo S, Qin X, Du G (2015) Analysis of Polygala tenuifolia transcriptome and description of secondary metabolite biosynthetic pathways by illumina sequencing. Int J Genomics 2015:782635. https://doi.org/10.1155/2015/782635
Tian X, Zhang Y, Li Z, Hu P, Chen M, Sun Z, Lin Y, Pan G, Huang C (2016) Systematic and comprehensive strategy for metabolite profiling in bioanalysis using software-assisted HPLC-Q-TOF: magnoflorine as an example. Anal Bioanal Chem 408(9):2239–2254. https://doi.org/10.1007/s00216-015-9254-5
Tian S, Jiang L, Gao Q, Zhang J, Zong M, Zhang H, Ren Y, Guo S, Gong G, Liu F, Xu Y (2017) Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Rep 36(3):399–406. https://doi.org/10.1007/s00299-016-2089-5
Tianniam S, Tarachiwin L, Bamba T, Kobayashi A, Fukusaki E (2008) Metabolic profiling of Angelica acutiloba roots utilizing gas chromatography-time-of-flight-mass spectrometry for quality assessment based on cultivation area and cultivar via multivariate pattern recognition. J Biosci Bioeng 105:655–659. https://doi.org/10.1263/jbb.105.655
Tikhomiroff C, Jolicoeur M (2002) Screening of Catharanthus roseus secondary metabolites by high-performance liquid chromatography. J Chromatogr A 955(1):87–93. https://doi.org/10.1016/s0021-9673(02)00204-2
Tohge T, Fernie AR (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 5(6):1210–1227. https://doi.org/10.1038/nprot.2010.82
Tohge T, Yonekura-Sakakibara K, Niida R, Watanabe-Takahashi A, Saito K (2007) Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis genes. Pure Appl Chem 79(4):811–823. https://doi.org/10.1351/pac200779040811
Tuli L, Ressom HW (2009) LC–MS based detection of differential protein expression. J Proteomics Bioinform 2(10):416–438. https://doi.org/10.4172/jpb.1000102
Turner MF, Heuberger AL, Kirkwood JS, Collins CC, Wolfrum EJ, Broeckling CD, Prenni JE, Jahn CE (2016) Non-targeted metabolomics in diverse Sorghum breeding lines indicates primary and secondary metabolite profiles are associated with plant biomass accumulation and photosynthesis. Front Plant Sci 7:953. https://doi.org/10.3389/fpls.2016.00953
Tzin V, Snyder JH, Yang DS, Huhman DV, Watson BS, Allen SN, Tang Y, Miettinen K, Arendt P, Pollier J, Goossens A, Sumner LW (2019) Integrated metabolomics identifies CYP72A67 and CYP72A68 oxidases in the biosynthesis of Medicago truncatula oleanate sapogenins. Metabolomics 15(6). https://doi.org/10.1007/s11306-019-1542-1
Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R (2015) Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol 15(1):212. https://doi.org/10.1186/s12870-015-0562-x
Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11(9):636–646. https://doi.org/10.1038/nrg2842
Van Wijk KJ (2001) Challenges and prospects of plant proteomics. Plant Physiol 126(2):501–508. https://doi.org/10.1104/pp.126.2.501
Vashisht I, Pal T, Sood H, Chauhan RS (2016) Comparative transcriptome analysis in different tissues of a medicinal herb, Picrorhiza kurroa pinpoints transcription factors regulating picrosides biosynthesis. Mol Biol Rep 43(12):1395–1409. https://doi.org/10.1007/s11033-016-4073-0
Veeresham C (2012) Natural products derived from plants as a source of drugs. J Adv Pharm Technol Res 3(4):200–201. https://doi.org/10.4103/2231-4040.104709
Verghese J (1993) Isolation of curcumin from Curcuma longa L. rhizome. Flavour Frag J 8(6):315–319. https://doi.org/10.1002/ffj.2730080605
Verpoorte R, Memelink J (2002) Engineering secondary metabolite production in plants. Curr Opin Biotechnol 13(2):181–187. https://doi.org/10.1016/s0958-1669(02)00308-7
Verpoorte R, Contin A, Memelink J (2002) Biotechnology for the production of plant secondary metabolites. Phytochem Rev 1(1):13–25. https://doi.org/10.1023/a:1015871916833
Volkov SK, Grodnitskaya EI (1994) Application of high-performance liquid chromatography to the determination of vinblastine in Catharanthus roseus. J Chromatogr B Biomed Sci Appl 660(2):405–408. https://doi.org/10.1016/0378-4347(94)00290-8
Wade OL (1986) Digoxin 1785-1985. I. Two hundred years of Digitalis. J Clin Hosp Pharm 11(1):3–9. https://doi.org/10.1111/j.1365-2710.1986.tb00822.x
Wang W, Wang Y, Zhang Q, Qi Y, Guo D (2009a) Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 10:465. https://doi.org/10.1186/1471-2164-10-465
Wang Z, Gerstein M, Snyder M (2009b) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. https://doi.org/10.1038/nrg2484
Wang Q, Reddy VA, Panicker D, Mao H-Z, Kumar N, Rajan C, Sarojam R (2016) Metabolic engineering of terpene biosynthesis in plants using a trichome-specific transcription factor MsYABBY5 from spearmint (Mentha spicata). Plant Biotechnol J 14(7):1619–1632. https://doi.org/10.1111/pbi.12525
Wang X, Xu Y, Zhang S, Cao L, Huang Y, Cheng J, Wu G, Tian S, Chen C, Liu Y, Yu H, Yang X, Lan H, Wang N, Wang L, Xu J, Jiang X, **e Z, Tan M, Larkin RM, Chen L-L, Ma B-G, Ruan Y, Deng X, Xu Q (2017) Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet 49(5):765–772. https://doi.org/10.1038/ng.3839
Wang W-W, Zheng C, Hao W-J, Ma C-L, Ma J-Q, Ni D-J, Chen L (2018) Transcriptome and metabolome analysis reveal candidate genes and biochemicals involved in tea geometrid defense in Camellia sinensis. PLoS One 13(8). https://doi.org/10.1371/journal.pone.0201670
Wang X, Liang H, Guo D, Guo L, Duan X, Jia Q, Hou X (2019) Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism. Hortic Res 6(1):111. https://doi.org/10.1038/s41438-019-0194-7
Wen W, Liu H, Zhou Y, ** M, Yang N, Li D, Luo J, **ao Y, Pan Q, Tohge T, Fernie AR, Yan J (2016) Combining quantitative genetics approaches with regulatory network analysis to dissect the complex metabolism of the Maize Kernel. Plant Physiol 170:136–146. https://doi.org/10.1104/pp.15.01444
Wielanek M, Urbanek H (1999) Glucotropaeolin and myrosinase production in hairy root cultures of Tropaeolum majus. Plant Cell Tissue Organ Cult 57:39–45. https://doi.org/10.1023/A:1006398902248
Wielanek M, Królicka A, Bergier K, Gajewska E, Skłodowska M (2009) Transformation of Nasturtium officinale, Barbarea verna and Arabis caucasica for hairy roots and glucosinolate-myrosinase system production. Biotechnol Lett 31:917–921. https://doi.org/10.1007/s10529-009-9953-0
Wilson SA, Roberts SC (2014) Metabolic engineering approaches for production of biochemicals in food and medicinal plants. Curr Opin Biotechnol 26:174–182. https://doi.org/10.1016/j.copbio.2014.01.006
Wittstock U, Burow M (2010) Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance. Arabidopsis Book 8. https://doi.org/10.1199/tab.0134
Wold JK (1978) Bound morphine and codeine in the capsule of Papaver somniferum. Phytochemistry 17(4):832–833. https://doi.org/10.1016/s0031-9422(00)94257-2
Wu Q, Song J, Sun Y, Suo F, Li C, Luo H, Liu Y, Li Y, Zhang X, Yao H, Li X, Hu S, Sun C (2010) Transcript profiles of Panax quinquefolius from flower, leaf and root bring new insights into genes related to ginsenosides biosynthesis and transcriptional regulation. Physiol Plant 138(2):134–139. https://doi.org/10.1111/j.1399-3054.2009.01309.x
Wurtele ES, Chappell J, Jones AD, Celiz MD, Ransom N, Hur M, Rizshsky L, Crispin M, Dixon P, Liu J, Widrlechner MP, Nikolau BJ (2012) Medicinal plants: a public resource for metabolomics and hypothesis development. Meta 2:1031–1059. https://doi.org/10.3390/metabo2041031
**n J, Zhang R, Wang L, Zhang Y (2017) Researches on transcriptome sequencing in the study of traditional Chinese medicine. Evid Based Complement Alternat Med 2017. https://doi.org/10.1155/2017/7521363
Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, Xu J, Li Y, Song C, Wang B, Sun W, Shen G, Zhang X, Qian J, Ji A, Xu Z, Luo X, He L, Li C, Sun C, Yan H, Cui G, Li X, Li X, Wei J, Liu J, Wang Y, Hayward A, Nelson D, Ning Z, Peters RJ, Qi X, Chen S (2016) Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza. Mol Plant 9(6):949–952. https://doi.org/10.1016/j.molp.2016.03.010
Yadav M, Chatterji S, Gupta SK, Watal G (2014) Preliminary phytochemical screening of six medicinal plants used in traditional medicine. Int J Pharm Pharm Sci 6(5):539–542
Yadav R, Kumar V, Baweja M, Shukla P (2017) Gene editing and genetic engineering approaches for advanced probiotics: a review. Crit Rev Food Sci 58(10):1735–1746. https://doi.org/10.1080/10408398.2016.1274877
Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, Yamaguchi H, Sasaki N, Miyahara T, Nishizaki Y, Ozeki Y, Nakamura N, Suzuki T, Tanaka Y, Sato S, Shirasawa K, Isobe S, Miyamura Y, Watanabe A, Nakayama S, Kishida Y, Kohara M, Tabata S (2014) Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Res 21(3):231–241. https://doi.org/10.1093/dnares/dst053
Yamazaki M, Rai A, Yoshimoto N, Saito K (2018) Perspective: functional genomics towards new biotechnology in medicinal plants. Plant Biotechnol Rep 12(2):69–75. https://doi.org/10.1007/s11816-018-0476-9
Yang L, Yang C, Li C, Zhao Q, Liu L, Fang X, Chen X-Y (2016) Recent advances in biosynthesis of bioactive compounds in traditional Chinese medicinal plants. Sci Bull 61(1):3–17. https://doi.org/10.1007/s11434-015-0929-2
Yang J, Jia M, Guo J (2019a) Functional genome of medicinal plants. In: Molecular pharmacognosy. Springer, Singapore, pp 191–234
Yang Z, Huang Y, An W, Zheng X, Huang S, Liang L (2019b) Sequencing and structural analysis of the complete chloroplast genome of the medicinal plant Lycium chinense Mill. Plants 8(4):87. https://doi.org/10.3390/plants8040087
Yao R, Heinrich M, Zou Y, Reich E, Zhang X, Chen Y, Weckerle CS (2018) Quality variation of goji (Fruits of Lycium spp.) in China: a comparative morphological and metabolomic analysis. Front Pharmacol 9(151). https://doi.org/10.3389/fphar.2018.00151
Ye W, Wu H, He X, Wang L, Zhang W, Li H, Fan Y, Tan G, Liu T, Gao X (2015) Transcriptome sequencing of chemically induced Aquilaria sinensis to identify genes related to agarwood formation. PLoS One 11(5). https://doi.org/10.1371/journal.pone.0155505
Yeh C-C, Hsu C-H, Shao Y-Y, Ho W-C, Tsai M-H, Feng W-C, Chow L-P (2015) Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) quantitative proteomic analysis identifies Galectin-1 as a potential biomarker for predicting sorafenib resistance in liver cancer. MCP 14(6):1527–1545. https://doi.org/10.1074/mcp.m114.046417
Yonemitsu H, Shimomura K, Satake M, Mochida S, Tanaka M, Endo T, Kaji A (1990) Lobeline production by hairy root culture of Lobelia inflata L. Plant Cell Rep 9:307–310. https://doi.org/10.1007/BF00232857
Yu ZX, Li JX, Yang CQ, Hu WL, Wang LJ, Chen XY (2012) The Jasmonate-responsive AP2/ERF transcription factors AaERF1 and AaERF2 positively regulate artemisinin biosynthesis in Artemisia annua L. Mol Plant 5(2):353–365. https://doi.org/10.1093/mp/ssr087
Yuan Y, Song L, Li M, Li G, Chu Y, Ma L, Zhou Y, Wang X, Gao W, Qin S, Yu J, Wang X, Huang L (2012) Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. BMC Genomics 13(1):195. https://doi.org/10.1186/1471-2164-13-195
Zaman QU, Li C, Cheng H, Hu Q (2019) Genome editing opens a new era of genetic improvement in polyploid crops. Crop J 7(2):141–150. https://doi.org/10.1016/j.cj.2018.07.004
Zeng S, **ao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.)Maxim. BMC Genomics 11(1). https://doi.org/10.1186/1471-2164-11-94
Zhan C, Li X, Zhao Z, Yang T, Wang X, Luo B, Zhang Q, Hu Y, Hu X (2016) Comprehensive analysis of the triterpenoid saponins biosynthetic pathway in Anemone flaccida by transcriptome and proteome profiling. Front Plant Sci 7:1094. https://doi.org/10.3389/fpls.2016.01094
Zhang HC, Liu JM, Lu HY, Gao SL (2009) Enhanced flavonoid production in hairy root cultures of Glycyrrhiza uralensis Fisch by combining the over-expression of chalcone isomerase gene with the elicitation treatment. Plant Cell Rep 28:1205–1213. https://doi.org/10.1007/s00299-009-0721-3
Zhang M, Wang F, Li S, Wang Y, Bai Y, Xu X (2014a) TALE: a tale of genome editing. Prog Biophys Mol 114(1):25–32. https://doi.org/10.1016/j.pbiomolbio.2013.11.006
Zhang P, Seth A, Fernandes H (2014b) Other post-PCR detection technologies. In: Pathobiology of human disease. Academic Press, London, pp 4074–4088
Zhang C, Wohlhueter R, Zhang H (2016a) Genetically modified foods: a critical review of their promise and problems. Food Sci Human Wellness 5(3):116–123. https://doi.org/10.1016/j.fshw.2016.04.002
Zhang GH, Jiang NH, Song WL, Ma CH, Yang SC, Chen JW (2016b) De novo sequencing and transcriptome analysis of Pinellia ternata identify the candidate genes involved in the biosynthesis of benzoic acid and ephedrine. Front Plant Sci 7:1209. https://doi.org/10.3389/fpls.2016.01209
Zhao W, Sheng S, Liu Z, Lu D, Zhu K, Li X, Zhao S, Yao Y (2014a) Isolation of biosynthesis related transcripts of 2,3,5,4′-tetrahydroxy stilbene-2-O-β-D-glucoside from Fallopia multiflora by suppression subtractive hybridization. Acta Soc Bot Pol 83(2):147–157. https://doi.org/10.5586/asbp.2014.012
Zhao W, **a W, Li J, Sheng S, Lei L, Zhao S (2014b) Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4′-tetrahydroxy stilbene-2-O-𝛽-d-glucoside. Gene 547:126–135
Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR (2017) De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin. GigaScience 6(9). https://doi.org/10.1093/gigascience/gix065
Zhao J, Li H, Yin Y, An W, Qin X, Wang Y, Li Y, Fan Y, Cao Y (2020) Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. Sci Rep 10. https://doi.org/10.1038/s41598-020-61064-5
Zhou JZ, Kou X, Stevenson D (1999) Rapid extraction and high-performance liquid chromatographic determination of parthenolide in feverfew (Tanacetum parthenium). J Agric Food Chem 47:1018–1022
Zhou H, Liu B, Weeks DP, Spalding MH, Yang B (2014) Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res 42(17):10903–10914. https://doi.org/10.1093/nar/gku806
Zhou Z, Tan H, Li Q, Chen J, Gao S, Wang Y, Chen W, Zhang L (2018) CRISPR/Cas9-mediated efficient targeted mutagenesis of RAS in Salvia miltiorrhiza. Phytochemistry 148:63–70. https://doi.org/10.1016/j.phytochem.2018.01.015
Zhou T, Luo X, Zhang C, Xu X, Yu C, Jiang Z, Zhang L, Yuan H, Zheng B, Pi E, Shen C (2019) Comparative metabolomic analysis reveals the variations in taxoids and flavonoids among three Taxus species. BMC Plant Biol 19. https://doi.org/10.1186/s12870-019-2146-7
Zhu Q-H, Wang M-B (2012) Molecular functions of long non-coding RNAs in plants. Genes 3(1):176–190. https://doi.org/10.3390/genes3010176
Zhu Y, Zhu G, Guo Q, Zhu Z, Wang C, Liu Z (2013) A comparative proteomic analysis of Pinellia ternata leaves exposed to heat stress. Int J Mol Sci 14:20614–20634. https://doi.org/10.3390/ijms141020614
Zhuang J, Zhang J, Hou X-L, Wang F, **ong A-S (2014) Transcriptomic, proteomic, metabolomic and functional genomic approaches for the study of abiotic stress in vegetable crops. Crit Rev Plant Sci 33(2–3):225–237. https://doi.org/10.1080/07352689.2014.870420
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Vijay, A. et al. (2022). Emergence of Phytochemical Genomics: Integration of Multi-Omics Approaches for Understanding Genomic Basis of Phytochemicals. In: Swamy, M.K., Kumar, A. (eds) Phytochemical Genomics. Springer, Singapore. https://doi.org/10.1007/978-981-19-5779-6_9
Download citation
DOI: https://doi.org/10.1007/978-981-19-5779-6_9
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-19-5778-9
Online ISBN: 978-981-19-5779-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)