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Multi-Omics Approaches for Breeding in Medicinal Plants

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Sustainable Agriculture in the Era of the OMICs Revolution

Abstract

Over the last few eras, multi-omics has been a successful technique for medicinal plants. All over the medicinal plants have been operated in ethnomedicine or traditional medicine. The modern multi-omics is a tool that has proved as most functional for complete knowledge of genomics, transcriptomics, and metabolism of medicinal plants. These medicinal plants showed novel regulators, compounds, secondary metabolites, and pathways through this comprehensive information from proteome, genome, transcriptome, and metabolome. This chapter presents a glimpse of the current status of further trends in medicinal plants. The panomics also allows the complex omics to construct the models that can assess the complex traits. The multi-omics datasets can enhance the understanding of crop improvement. This chapter describes an advancement in multi-omics research areas and involves utilizing medicinal plants with medicinal values around the globe.

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References

  • Alsemari, A., Alkhodairy, F., Aldakan, A., Al-Mohanna, M., Bahoush, E., Shinwari, Z., & Alaiya, A. (2014). The selective cytotoxic anticancer properties and proteomic analysis of Trigonella foenum-graecum. BMC Complementary and Alternative Medicine, 14, 114.

    Article  Google Scholar 

  • Anantachoke, N., Tuchinda, P., Kuhakarn, C., Pohmakotr, M., & Reutrakul, V. (2012). Prenylated caged xanthones: Chemistry and biology. Pharmaceutical Biology, 50, 78–91.

    Article  CAS  Google Scholar 

  • Aneesh, T. P., Hisham, M., Sekhar, S., Madhu, M., & Deepa, T. V. (2009). International market scenario of traditional Indian herbal drugs – India declining. International Journal of Green Pharmacy (IJGP), 3(3), 184–190.

    Article  Google Scholar 

  • Annadurai, R. S., Neethiraj, R., Jayakumar, V., Damodaran, A. C., Rao, S. N., & Katta, M. A. (2021). Crosstalk of multi-omics platforms with plants of therapeutic importance. Cells, 10, 1296.

    Article  Google Scholar 

  • Baharum, S. N., Bunawan, H., Ghani, M. A., Wan Aida Wan, M., & Noor, N. M. (2010). Analysis of the chemical composition of the essential oil of Polygonum minus Huds. Using two-dimensional gas chromatography-time-of-flight mass spectrometry (GC-TOF MS). Molecules, 15, 7006–7015.

    Article  CAS  Google Scholar 

  • Bandaranayake, W. M. (2006). Quality control, screening, toxicity, and regulation of herbal drugs. In I. Ahmad, F. Aqil, & M. Owais (Eds.), Modern phytomedicine: turning medicinal plants into drugs (pp. 25–57). Wiley-VCH.

    Chapter  Google Scholar 

  • Biswas, K., & Biswas, R. (2014). DNA molecular markers based authentication of herbal drugs-A review. International Journal for Pharmaceutical Research, 3, 581–593.

    Google Scholar 

  • Boutanaev, A. M., Moses, T., Zi, J., Nelson, D. R., Mugford, S. T., Peters, R. J., & Osbourn, A. (2015). Investigation of terpene diversification across multiple sequenced plant genomes. Proceedings of the National Academy of Sciences, 112(1), E81–E88.

    Article  CAS  Google Scholar 

  • Bovy, A., Schijlen, E., & Hall, R. D. (2007). Metabolic engineering of flavonoids in tomato: The potential for metabolomics. Metabolomics, 3, 399–412.

    Article  CAS  Google Scholar 

  • Briskin, D. P. (2000). Medicinal plants and phytomedicines. Linking plant biochemistry and physiology to human health. Plant Physiology, 124(2), 507–514.

    Article  CAS  Google Scholar 

  • Brusotti, G., Cesari, I., Dentamaro, A., Caccialanza, G., & Massolini, G. (2014). Isolation and characterization of bioactive compounds from plant resources: the role of analysis in the ethnopharmacological approach. Journal of Pharmaceutical and Biomedical Analysis, 87, 218–228.

    Article  CAS  Google Scholar 

  • Buckingham-Meyer, K., Goeres, D. M., & Hamilton, M. A. (2007). Comparative evaluation of biofilm disinfectant efficacy tests. Journal of Microbiological Methods, 70(2), 236–244.

    Google Scholar 

  • Bunsupa, S., Katayama, K., Ikeura, E., Oikawa, A., Toyooka, K., Saito, K., & Yamazaki, M. (2012). Lysine decarboxylase catalyzes the first step of quinolizidine alkaloid biosynthesis and coevolved with alkaloid production in Leguminosae. Plant Cell, 24, 1202–1216.

    Article  CAS  Google Scholar 

  • Busian, K., & Kasilo, O. M. (2010). Overview of traditional medicine in ECOWAS member states. African Health Monitor.

    Google Scholar 

  • Cai, X., Fang, Z., Dou, J., Yu, A., & Zhai, G. (2013). Bioavailability of quercetin: problems and promises. Current Medicinal Chemistry, 20(20), 2572–2582.

    Google Scholar 

  • Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W. C., Liu, K. W., et al. (2015). The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics, 47(1), 65–72.

    Article  CAS  Google Scholar 

  • Cámara-Leret, R., Faurby, S., Macía, M. J., Balslev, H., Göldel, B., Svenning, J. C., et al. (2017). Fundamental species traits explain provisioning services of tropical American palms. Nature Plants, 3(2), 1–7.

    Article  Google Scholar 

  • Cannon, S. B., McKain, M. R., Harkess, A., Nelson, M. N., Dash, S., Deyholos, M. K., Peng, Y., Joyce, B., Stewart, C. N., Jr., & Rolf, M. (2015). Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. Molecular Biology and Evolution, 32, 193–210.

    Article  CAS  Google Scholar 

  • Chakraborty, P. (2018). Herbal genomics as tools for dissecting new metabolic pathways of unexplored medicinal plants and drug discovery. Biochimie Open, 6, 9–16.

    Article  Google Scholar 

  • Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., et al. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345(6199), 950–953.

    Article  CAS  Google Scholar 

  • Chantarasriwong, O., Batova, A., Chavasiri, W., & Theodorakis, E. A. (2010). Chemistry and biology of the caged Garcinia xanthones. Chemistry – A European Journal, 16, 9944–9962.

    Article  CAS  Google Scholar 

  • Chen, J. T. (2020). Phytochemical omics in medicinal plants. Biomolecules, 10(6), 936.

    Article  CAS  Google Scholar 

  • Chen, S., Sun, Y., Xu, J., Luo, H., Sun, C., He, L., et al. (2010). Strategies of the study on herb genome program. Yao Xue Bao Acta Pharmaceutica Sinica, 45(7), 807–812.

    Google Scholar 

  • Chen, T., Zhang, R. H., He, S. C., Xu, Q. Y., Ma, L., Wang, G. C., Qiu, N., Peng, F., Chen, J. Y., Qiu, J. X., et al. (2012). Synthesis and antiangiogenic activity of novel gambogic acid derivatives. Molecules, 17, 6249–6268.

    Article  CAS  Google Scholar 

  • Chen, S., Song, J., Sun, C., Xu, J., Zhu, Y., Verpoorte, R., & Fan, T. P. (2015). Herbal genomics: examining the biology of traditional medicines. Science, 347(6219), S27–S29.

    Google Scholar 

  • Chen, M., Yan, T., Ji, L., Dong, Y., Sidoli, S., Yuan, Z., Cai, C., Chen, J., Tang, Y., Shen, Q., et al. (2020). Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin. Proteomics, 20, e1900310.

    Article  Google Scholar 

  • Chen, K., Yin, Y., Liu, S., Guo, Z., Zhang, K., Liang, Y., ... & Li, M. (2019). Genome-wide identification and functional analysis of oleosin genes in Brassica napus L. BMC Plant Biology, 19(1), 1–20.

    Google Scholar 

  • Chen, S. L., Yu, H., Luo, H. M., Wu, Q., Li, C. F., & Steinmetz, A. (2016). Conservation and sustainable use of medicinal plants: problems, progress, and prospects. Chinese Medicine, 11(1), 1–10.

    Article  Google Scholar 

  • Chu, H. Y., Wegel, E., & Osbourn, A. (2011). From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. The Plant Journal, 66(1), 66–79.

    Article  CAS  Google Scholar 

  • Costion, C., Ford, A., Cross, H., Crayn, D., Harrington, M., & Lowe, A. (2011). Plant DNA barcodes can accurately estimate species richness in poorly known floras. PLoS ONE, 6(11), e26841.

    Article  CAS  Google Scholar 

  • Cragg, G. M., & Newman, D. J. (2013). Natural products: A continuing source of novel drug leads. Biochimica et Biophysica Acta, 1830, 3670–3695.

    Article  CAS  Google Scholar 

  • Cramer, G. R., Urano, K., Delrot, S., Pezzotti, M., & Shinozaki, K. (2011). Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biology, 11(1), 1–14.

    Google Scholar 

  • Croteau, R., Kutchan, T. M., & Lewis, N. G. (2000). Natural products (Secondary metabolites). Biochemistry and Molecular Biology of Plants, 24, 1250–1319.

    Google Scholar 

  • Cui, G., Huang, L., Tang, X., & Zhao, J. (2011). Candidate genes involved in tanshinone biosynthesis in hairy roots of Salvia miltiorrhiza revealed by cDNA microarray. Molecular Biology Reports, 38, 2471–2478.

    Article  CAS  Google Scholar 

  • Daldoul, S., Amar, A. B., Guillaumie, S., & Mliki, A. (2014). Integration of omics and system biology approaches to study grapevine (Vitis vinifera L.) response to salt stress: a perspective for functional genomics-a review. Oeno One, 48(3), 189–200.

    Google Scholar 

  • De Luca, V., Salim, V., Atsumi, S. M., & Yu, F. (2012). Mining the biodiversity of plants: a revolution in the making. Science, 336(6089), 1658–1661.

    Article  Google Scholar 

  • Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., et al. (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345(6201), 1181–1184.

    Article  CAS  Google Scholar 

  • Dinda, B., Chowdhury, R., & Mohanta, D. (2009). Naturally occurring iridoids, secoiridoids and their bioactivity. Chemical & Pharmaceutical Bulletin, 57, 765–796.

    Article  CAS  Google Scholar 

  • Dinda, B., Debnath, S., & Banik, R. (2011). Naturally occurring iridoids and secoiridoids. Chemical & Pharmaceutical Bulletin, 59, 803–833.

    Article  CAS  Google Scholar 

  • Dinda, S., Patwardhan, A. V., Goud, V. V., & Pradhan, N. C. (2008). Epoxidation of cottonseed oil by aqueous hydrogen peroxide catalysed by liquid inorganic acids. Bioresource Technology, 99(9), 3737–3744.

    Google Scholar 

  • Dixon, R. A., & Strack, D. (2003). Phytochemistry meets genome analysis, and beyond. Phytochemistry, 62, 815–816.

    Article  CAS  Google Scholar 

  • El-Naggar, S. A., Abdel-Farid, I. B., Elgebaly, H. A., & Germoush, M. O. (2015). Metabolomic profiling, antioxidant capacity and in vitro anticancer activity of some compositae plants growing in Saudi Arabia. African Journal of Pharmacy and Pharmacology, 9, 764–774.

    Article  CAS  Google Scholar 

  • Facchini, P. J., Bohlmann, J., Covello, P. S., De Luca, V., Mahadevan, R., Page, J. E., Ro, D. K., Sensen, C. W., Storms, R., & Martin, V. J. (2012). Synthetic biosystems for the production of high-value plant metabolites. Trends in Biotechnology, 30, 127–131.

    Article  CAS  Google Scholar 

  • Fang, H. Y., Chen, S. B., Guo, D. J., Pan, S. Y., & Yu, Z. L. (2011). Proteomic identification of differentially expressed proteins in curcumin-treated MCF-7 cells. Phytomedicine, 18, 697–703.

    Article  Google Scholar 

  • Fang, X., Chen, W., Xin, Y., Zhang, H., Yan, C., Yu, H., ... & Ruan, S. (2012). Proteomic analysis of strawberry leaves infected with Colletotrichum fragariae. Journal of Proteomics, 75(13), 4074–4090.

    Google Scholar 

  • Farnsworth, N. R. (1988). Screening plants for new medicines. Biodiversity, 15(3), 81–99.

    Google Scholar 

  • Field, B., Fiston-Lavier, A. S., Kemen, A., Geisler, K., Quesneville, H., & Osbourn, A. E. (2011). Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proceedings of the National Academy of Sciences of the United States of America, 108, 16116–16121.

    Article  CAS  Google Scholar 

  • Fiehn, O. (2002). Metabolomics—the link between genotypes and phenotypes. Functional Genomics, 155–171.

    Google Scholar 

  • Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014). Pfam: the protein families database. Nucleic Acids Research, 42, 222–230.

    Article  Google Scholar 

  • Freeling, M., & Subramaniam, S. (2009). Conserved noncoding sequences (CNSs) in higher plants. Current opinion in plant biology, 12(2), 126–132.

    Google Scholar 

  • Fu, W. M., Zhang, J. F., Wang, H., Tan, H. S., Wang, W. M., Chen, S. C., Zhu, X., Chan, T. M., Tse, C. M., Leung, K. S., et al. (2012a). Apoptosis induced by 1,3,6,7-tetrahydroxy xanthone in Hepatocellular carcinoma and proteomic analysis. Apoptosis, 12, 842–851.

    Article  Google Scholar 

  • Fu, W. M., Zhang, J. F., Wang, H., Xi, Z. C., Wang, W. M., Zhuang, P., Zhu, X., Chen, S. C., Chan, T. M., Leung, K. S., et al. (2012b). Heat shock protein 27 mediates the effect of 1,3,5-trihydroxy-13,13-dimethyl-2H- pyran [7,6-b] xanthone on mitochondrial apoptosis in hepatocellular carcinoma. Journal of Proteomics, 75, 4833–4843. Cells 2021, 10, 1296 22 of 23.

    Article  CAS  Google Scholar 

  • García-Alcalde, F., García-López, F., Dopazo, J., & Conesa, A. (2011). Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics, 27(1), 137–139.

    Google Scholar 

  • Gagne, S. J., Stout, J. M., Liu, E., Boubakir, Z., Clark, S. M., & Page, J. E. (2012). Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proceedings of the National Academy of Sciences of the United States of America, 109, 1281–1286.

    Google Scholar 

  • Gahlaut, A., Dahiya, M., Gothwal, A., Kulharia, M., Chhillar, A. K., Hooda, V., & Dabur, R. (2013). Proteomics & metabolomics: Mapping biochemical regulations. Drug Invention Today, 5(4), 321–326.

    Article  CAS  Google Scholar 

  • Gesell, A., Rolf, M., Ziegler, J., Chávez, M. L. D., Huang, F. C., & Kutchan, T. M. (2009). CYP719B1 is salutaridine synthase, the CC phenol-coupling enzyme of morphine biosynthesis in opium poppy. Journal of Biological Chemistry, 284(36), 24432–24442.

    Article  CAS  Google Scholar 

  • Geu-Flores, F., Sherden, N. H., Courdavault, V., Burlat, V., Glenn, W. S., Wu, C., Nims, E., Cui, Y., & O’Connor, S. E. (2012). An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature, 492, 138–142.

    Article  CAS  Google Scholar 

  • Giddings, L. A., Liscombe, D. K., Hamilton, J. P., Childs, K. L., DellaPenna, D., Buell, C. R., & O’Connor, S. E. (2011). A stereo selective hydroxylation step of alkaloid biosynthesis by a unique cytochrome P450 in Catharanthus roseus. The Journal of Biological Chemistry, 286, 16751–16757.

    Article  CAS  Google Scholar 

  • Global Industry Analysts (GIA). (2015). Inc. report on the global herbal supplements and remedies market trends drivers & projections. Available online: http://www.strategyr.com/marketresearch/herbalsupplementsandremediesmarkettrends.asp. Accessed 15 Feb 2015.

  • Goh, H. H., Khairudin, K., Sukiran, N. A., Normah, M. N., & Baharum, S. N. (2016). Metabolite profiling reveals temperature effects on the VOCs and flavonoids of different plant populations. Plant Biology, 18, 130–139.

    Article  CAS  Google Scholar 

  • Gongora-Castillo, E., McKnight, T. D., O’Connor, S., Childs, K. L., Buell, C., Fedewa, G., Hamilton, J. P., Liscombe, D. K., MagallanesLundback, M., Mandadi, K. K., et al. (2012). Development of transcriptomic resources for interrogating the biosynthesis of monoterpeneindole alkaloids in medicinal plant species. PLoS ONE, 7, e52506.

    Article  CAS  Google Scholar 

  • Grimplet, J., Cramer, G. R., Dickerson, J. A., Mathiason, K., Van Hemert, J., & Fennell, A. Y. (2009). VitisNet: “Omics” integration through grapevine molecular networks. PLoS ONE, 4, e8365.

    Article  Google Scholar 

  • Guo, R., Shi, L., Yan, C., Zhong, X., Gu, F., Liu, Q., ... & Li, H. (2017). Ionomic and metabolic responses to neutral salt or alkaline salt stresses in maize (Zea mays L.) seedlings. BMC Plant Biology, 17(1), 1–13.

    Google Scholar 

  • Gupta, P., Goel, R., Agarwal, A. K., Asif, M. H., Sangwan, N. S., Sangwan, R. S., & Trivedi, P. K. (2015). Comparative tran-scriptome analysis of different chemotypes elucidates withanolide biosynthesis pathway from medicinal plant Withania somnifera. Scientific Reports, 5, 1861.

    Article  Google Scholar 

  • Gupta, B., Sengupta, A., Saha, J., & Gupta, K. (2013). Plant abiotic stress:‘Omics’ approach. Journal of Plant Biochemistry and Physiology, 1(3), 10–4172.

    Google Scholar 

  • Hagel, J. M., & Facchini, P. J. (2010). Dioxygenases catalyze the O-demethylation steps of morphine biosynthesis in opium poppy. Nature Chemical Biology, 6(4), 273–275.

    Article  CAS  Google Scholar 

  • Hale, V., Keasling, J. D., Renninger, N., & Diagana, T. T. (2007). Microbially derived artemisinin: A biotechnology solution to the global problem of access to affordable antimalarial drugs. The American Journal of Tropical Medicine and Hygiene, 77(6_Suppl), 198–202.

    Article  Google Scholar 

  • Hao, D. C., & Xiao, P. G. (2015). Genomics and evolution in traditional medicinal plants: Road to a healthier life. Evolutionary Bioinformatics, 11, EBO-S31326.

    Article  Google Scholar 

  • Hao, D. C., Ge, G., Xiao, P., Zhang, Y., & Yang, L. (2011). The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing. PLoS ONE, 6, e21220.

    Article  CAS  Google Scholar 

  • Hao, L. H., Wang, W. X., Chen, C., Wang, Y. F., Liu, T., Li, X., & Shang, Z. L. (2012). Extracellular ATP promotes stomatal opening of Arabidopsis thaliana through heterotrimeric G protein α subunit and reactive oxygen species. Molecular Plant, 5(4), 852–864.

    Google Scholar 

  • Hao, D. C., Xiao, P. G., Liu, M., Peng, Y., & He, C. N. (2014). Pharmaphylogeny vs. pharmacophylogenomics: Molecular phylogeny, evolution and drug discovery. Yao Xue Bao, 49, 1387–1394.

    CAS  Google Scholar 

  • Hao, Y. H., Fountain Jr, M. D., Tacer, K. F., Xia, F., Bi, W., Kang, S. H. L., ... & Potts, P. R. (2015). USP7 acts as a molecular rheostat to promote WASH-dependent endosomal protein recycling and is mutated in a human neurodevelopmental disorder. Molecular Cell, 59(6), 956–969.

    Google Scholar 

  • Hao, D. C., He, C. N., Shen, J., & Xiao, P. G. (2017). Anticancer chemodiversity of Ranunculaceae medicinal plants: Molecular mecha-nisms and functions. Current Genomics, 18, 39–59.

    Article  CAS  Google Scholar 

  • Hartmann, T. (2007). From waste products to ecochemicals: Fifty years research of plant secondary metabolism. Phytochemistry, 68, 2831–2846.

    Article  CAS  Google Scholar 

  • Hartmann-Boyce, J., Chepkin, S. C., Ye, W., Bullen, C., & Lancaster, T. (2018). Nicotine replacement therapy versus control for smoking cessation. Cochrane Database of Systematic Reviews, 5, CD000146.

    Google Scholar 

  • He, Y., Xiao, H., Deng, C., Xiong, L., Yang, J., & Peng, C. (2016). The complete chloroplast genome sequences of the medicinal plant Pogostemon cablin. International Journal of Molecular Sciences, 17, 820–830.

    Article  Google Scholar 

  • Hirai, M. Y., Yano, M., Goodenowe, D. B., Kanaya, S., Kimura, T., Awazuhara, M., Arita, M., Fujiwara, T., & Saito, K. (2004). Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 101(27), 10205-10210.

    Google Scholar 

  • Hollister, J. D., Greiner, S., Wang, W., Wang, J., Zhang, Y., Wong, G. K., Wright, S. I., & Johnson, M. T. (2015). Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera. Molecular Biology and Evolution, 32, 896–905.

    Article  CAS  Google Scholar 

  • Hong, L., Qian, Q., Tang, D., Wang, K., Li, M., & Cheng, Z. (2012). A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype. Planta, 236, 141–151.

    Article  CAS  Google Scholar 

  • Huang, W. S., Kuo, Y. H., Chin, C. C., Wang, J. Y., Yu, H. R., Sheen, J. M., Tung, S. Y., Shen, C. H., Chen, T. C., & Sung, M. L. (2012). Proteomic analysis of the effects of baicalein on colorectal cancer cells. Proteomics, 12, 810–819.

    Article  CAS  Google Scholar 

  • Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., et al. (2012). InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research, 40, 306–312.

    Article  Google Scholar 

  • Hyun, T. K., Lee, S., Rim, Y., Kumar, R., Han, X., Lee, S. Y., ... & Kim, J. Y. (2014). De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel). PLoS ONE, 9(2), e88292.

    Google Scholar 

  • Jaillon, O., Aury, J. M., Noel, B., Policriti, A., Clepet, C., Cassagrande, A., et al. (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449(7161), 463–467.

    Article  CAS  Google Scholar 

  • Jenkins, C., & Orsburn, B. (2020). The Cannabis Proteome Draft Map Project. International Journal of Molecular Sciences, 21, 965.

    Article  CAS  Google Scholar 

  • Jiao, Y., & Paterson, A. H. (2014). Polyploidy-associated genome modifications during land plant evolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 369, 20130355.

    Article  Google Scholar 

  • Jiao, Y., Wickett, N. J., Ayyampalayam, S., Chanderbali, A. S., Landherr, L., Ralph, P. E., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature, 473(7345), 97–100.

    Article  CAS  Google Scholar 

  • Joshi, K., Ghodke, Y., & Shintre, P. (2010). Traditional medicine and genomics. Journal of Ayurveda and Integrative Medicine, 1(1), 26.

    Article  Google Scholar 

  • Jogaiah, S., Govind, S. R., & Tran, L. S. P. (2013). Systems biology-based approaches toward understanding drought tolerance in food crops. Critical Reviews in Biotechnology, 33(1), 23–39.

    Google Scholar 

  • Kaushal, N., Rao, S., Ghanghas, P., Abraham, S., George, T., D’souza, S., et al. (2018). Usefulness of Ocimum sanctum Linn. in cancer prevention: An update. In M. S. Akhtar & M. K. Swamy (Eds.), Anticancer plants: properties and application (pp. 415–429). Springer.

    Chapter  Google Scholar 

  • Kaushik, N. (2005). Saponins of Chlorophytum species. Phytochemistry Reviews, 4, 191–196.

    Article  CAS  Google Scholar 

  • Kellner, A. (2015). Genome sequence of Catharanthus roseus. Available online http://medicinalplantgenomics.msu.edu/. Accessed 25 Dec 2019.

  • Kellner, F., Kim, J., Clavijo, B. J., Hamilton, J. P., Childs, K. L., Vaillancourt, B., et al. (2015). Genome-guided investigation of plant natural product biosynthesis. The Plant Journal, 82(4), 680–692.

    Article  CAS  Google Scholar 

  • Kellner, M. J., Koob, J. G., Gootenberg, J. S., Abudayyeh, O. O., & Zhang, F. (2019). SHERLOCK: nucleic acid detection with CRISPR nucleases. Nature Protocols, 14(10), 2986–3012.

    Google Scholar 

  • 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. Frontiers in Pharmacology, 8, 474.

    Article  Google Scholar 

  • Kim, H. K., Wilson, E. G., Choi, Y. H., & Verpoorte, R. (2010). Metabolomics: A tool for anticancer lead-finding from natural products. Planta Medica, 76, 1094–1102.

    Article  CAS  Google Scholar 

  • Kim, S., Park, M., Yeom, S. I., Kim, Y. M., Lee, J. M., Lee, H. A., et al. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 46(3), 270–278.

    Article  CAS  Google Scholar 

  • Kim, Y. B., Komor, A. C., Levy, J. M., Packer, M. S., Zhao, K. T., & Liu, D. R. (2017). Increasing the genometargeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nature Biotechnology, 35(4), 371–376.

    Google Scholar 

  • Krishnan, N. M., Pattnaik, S., Jain, P., Gaur, P., Choudhary, R., Vaidyanathan, S., Deepak, S., Hariharan, A. K., Krishna, P. G. B., & Nair, J. (2012). A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genomics, 13, 464.

    Article  CAS  Google Scholar 

  • Ku, C., Chung, W. C., Chen, L. L., & Kuo, C. H. (2013). The complete plastid genome sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid genome evolution, molecular marker identification, and phylogenetic implications in Asterids. PLoS ONE, 8, e68518.

    Article  CAS  Google Scholar 

  • Kumar, M., Meena, P., Verma, S., Kumar, M., & Kumar, A. (2010). Anti-tumour, anti-mutagenic and chemomodulatory potential of Chlorophytum borivilianum. Asian Pacific Journal of Cancer Prevention, 11, 327–334.

    Google Scholar 

  • Kumar, A., Pathak, R. K., Gupta, S. M., Gaur, V. S., & Pandey, D. (2015). Systems biology for smart crops and agricultural innovation: filling the gaps between genotype and phenotype for complex traits linked with robust agricultural productivity and sustainability. Omics: A Journal of Integrative Biology, 19(10), 581–601.

    Google Scholar 

  • Kumar, V. V., Swamy, M. K., & Akhtar, M. (2018). Anticancer plants and their conservation strategies: an update. In M. S. Akhtar & M. K. Swamy (Eds.), Anticancer plants: properties and application (pp. 455–483). Springer.

    Chapter  Google Scholar 

  • Kumari, A., Das, P., Parida, A. K., & Agarwal, P. K. (2015). Proteomics, metabolomics, and ionomics perspectives of salinity tolerance in halophytes. Frontiers in Plant Science, 6, 537.

    Google Scholar 

  • Kuo, T. C., Tian, T. F., & Tseng, Y. J. (2013). 3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. BMC Systems Biology, 7(1), 1–15.

    Google Scholar 

  • Lao, Y., Wang, X., Xu, N., Zhang, H., & Xu, H. (2014). Application of proteomics to determine the mechanism of action of traditional Chinese medicine remedies. Journal of Ethnopharmacology, 155, 1–8.

    Article  CAS  Google Scholar 

  • Lau, W., & Sattely, E. S. (2015). Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science, 349, 1224–1228.

    Article  CAS  Google Scholar 

  • Li, Y., Xu, C., Lin, X., Cui, B., Wu, R., & Pang, X. (2014). De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PLoS ONE, 9(9), e106438.

    Article  Google Scholar 

  • Liu, Z., Ma, L., & Zhou, G. B. (2011). The main anticancer bullets of the Chinese medicinal herb, thunder God vine. Molecules, 16, 5283–5297.

    Article  CAS  Google Scholar 

  • Liu, W., Yin, D., Liu, J., & Li, N. (2014). Genetic diversity and structure of Sinopodophyl¬lum hexandrum (Royle) Ying in the Qinling Mountains, China. PLoS ONE, 9, e110500.

    Article  Google Scholar 

  • Lu, Z., Song, Q., Yang, J., Zhao, X., Zhang, X., Yang, P., & Kang, J. (2014). Comparative proteomic analysis of anti-cancer mechanism by periplocin treatment in lung cancer cells. Cellular Physiology and Biochemistry, 33, 859–868.

    Article  Google Scholar 

  • Luo, J., Hou, B. W., Niu, Z. T., Liu, W., Xue, Q. Y., & Ding, X. Y. (2014). Comparative chloroplast genomes of photosynthetic orchids: Insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications. PLoS ONE, 9, e99016.

    Article  Google Scholar 

  • Luo, X., Wang, J., Dooner, M., & Clarke, J. (2015). Overview of current development in electrical energy storage technologies and the application potential in power system operation. Applied Energy, 137, 511–536.

    Google Scholar 

  • Ma, Y., Yuan, L., Wu, B., Li, X., Chen, S., & Lu, S. (2012). Genome-wide identification and characterization of novel genes involved in terpenoid biosynthesis in Salvia miltiorrhiza. Journal of Experimental Botany, 63, 2809–2823.

    Article  CAS  Google Scholar 

  • Ma, X., Meng, Y., Wang, P., Tang, Z., Wang, H., & Xie, T. (2020). Bioinformatics-assisted, integrated omics studies on medicinal plants. Briefings in Bioinformatics, 21(6), 1857–1874.

    Article  CAS  Google Scholar 

  • Mahajan, R. T. C. M., & Chopda, M. (2009). Phyto-Pharmacology of Ziziphus jujuba Mill-A plant review. Pharmacognosy Reviews, 3(6), 320.

    CAS  Google Scholar 

  • Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J.I., Ebana, K., Yano, M. and Saito, K. (2015). Metabolome‐genome‐wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. The Plant Journal, 81(1), 13–23.

    Google Scholar 

  • Mehta, A., & Hasija, Y. (2018). Bioinformatics approaches for genomics and post genomics applications of anticancer plants. In M. S. Akhtar & M. K. Swamy (Eds.), Anticancer plants: Mechanisms and molecular interactions (pp. 283–317). Springer.

    Chapter  Google Scholar 

  • Mishra, P., Kumar, A., Nagireddy, A., Mani, D. N., Shukla, A. K., Tiwari, R., & Sundaresan, V. (2016). DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnology Journal, 14(1), 8–21.

    Article  CAS  Google Scholar 

  • Mochida, K., Sakurai, T., Seki, H., Yoshida, T., Takahagi, K., Sawai, S., et al. (2017). Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. The Plant Journal, 89(2), 181–194.

    Article  CAS  Google Scholar 

  • Modak, M., Dixit, P., Londhe, J., Ghaskadbi, S., & Devasagayam, T. P. A. (2007). Indian herbs and herbal drugs used for the treatment of diabetes. Journal of Clinical Biochemistry and Nutrition, 40(3), 163–173.

    Article  Google Scholar 

  • Mosa, K. A., Ismail, A., & Helmy, M. (2017). Omics and system biology approaches in plant stress research. In Plant stress tolerance (pp. 21–34). Springer, Cham.

    Google Scholar 

  • Muir, S. R., Collins, G. J., Robinson, S., Hughes, S., Bovy, A., Ric De Vos, C. H., van Tunen, A. J., & Verhoeyen, M. E. (2001). Overexpression of petunia chalcone isomerase in tomato results in fruit containing increased levels of flavonols. Nature Biotechnology, 19, 470–474.

    Article  CAS  Google Scholar 

  • Mukherjee, P. K., Harwansh, R. K., Bahadur, S., Biswas, S., Kuchibhatla, L. N., Tetali, S. D., & Raghavendra, A. S. (2016). Metabolomics of medicinal plants- a versatile tool for standardization of herbal products and quality evaluation of Ayurvedic formulations. Current Science, 111, 1624–1630.

    Article  CAS  Google Scholar 

  • Nagappan, A., Karunanithi, N., Sentrayaperumal, S., Park, K. I., Park, H. S., Lee, D. H., Kang, S. R., Kim, J. A., Senthil, K., Natesan, S., et al. (2012). Comparative root protein profiles of Korean ginseng (Panax ginseng) and Indian ginseng (Withania somnifera). The American Journal of Chinese Medicine, 40, 203–218.

    Article  CAS  Google Scholar 

  • Newman, D. J., & Cragg, G. M. (2016). Natural products as sources of new drugs from 1981 to 2014. Journal of Natural Products, 79, 629–661.

    Article  CAS  Google Scholar 

  • Nilsson, K., Sangster, M., & Konijnendijk, C. C. (2011). Forests, trees and human health and well-being: Introduction. In K. Nilsson, M. Sangster, C. Gallis, T. Hartig, S. de Vries, K. Seeland, & J. Schipperijn (Eds.), Forests, trees and human health (pp. 1–19). Springer.

    Chapter  Google Scholar 

  • Norton, G. J., Deacon, C. M., Xiong, L., Huang, S., Meharg, A. A., & Price, A. H. (2010). Genetic mapping of the rice ionome in leaves and grain: identification of QTLs for 17 elements including arsenic, cadmium, iron and selenium. Plant and Soil, 329(1), 139–153.

    Google Scholar 

  • Noorolahi, S. M., Sadeghi, S., Mohammadi, M., Azadi, M., Rahimi, N. A., Vahabi, F., Arjmand, M., Hosseini, H., Mosallatpur, S., & Zamani, Z (2016). Metabolomic profiling of cancer cells to Aloe vera extract by 1HNMR spectroscopy. Journal of Metabol, 2, pp.1–7.

    Google Scholar 

  • Okada, T., Mochamad Afendi, F., Altaf-Ul-Amin, M., Takahashi, H., Nakamura, K., & Kanaya, S. (2010). Metabolomics of medicinal plants: The importance of multivariate analysis of analytical chemistry data. Current Computer-Aided Drug Design, 6, 179–196.

    Article  CAS  Google Scholar 

  • Pandita, D., Pandita, A., & Pandita, S. (2013). Herbaceous medicinal & therapeutic plants of district samba of Jammu province, Jammu & Kashmir (India). International Journal of Indigenous Medicinal Plants, 46, 1224–1238.

    Google Scholar 

  • Pandita, D., Pandita, A., & Pandita, S. (2014). The revitalizing and recuperative higher Tracheophytes of Jammu province, Jammu and Kashmir (India). International Journal of Indigenous Medicinal Plants, 47(1), 1603–1620.

    Google Scholar 

  • Pandita, D., Pandita, A., & Pandita, S. (2015). Pharmacological and phytochemical portrayal of dicotyledonous medicinal plants of Jammu and Kashmir abound with antidiabetic potential. Journal of Microbiology and Biotechnology Research, 5, 16–27.

    CAS  Google Scholar 

  • Paterson, A. D., Waggott, D., Boright, A. P., Hosseini, S. M., Shen, E., Sylvestre, M. P., Wong, I., Bharaj, B., Cleary, P.A., Lachin, J. M., & MAGIC (Meta-Analyses of Glucose and Insulin-related traits Consortium). (2010). A genomewide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. Diabetes, 59(2), 539–549.

    Google Scholar 

  • Payne, G. F., Bringi, V., Prince, C., & Shuler, M. L. (1991). The quest for commercial production of chemicals from plant cell culture. In G. F. Payne, V. Bringi, C. Prince, & M. L. Shuler (Eds.), Plant cell and tissue culture in liquid systems (pp. 1–10). Hanser.

    Google Scholar 

  • Pinson, S. R. M., Tarpley, L., Yan, W., Yeater, K., Lahner, B., Yakubova, E., Huang, X. Y., Zhang, M., Guerinot, M.L., & Salt, D. E. (2015a). Worldwide genetic diversity for mineral element concentrations in rice grain. Crop Science, 55(1), 294–311.

    Google Scholar 

  • Pinson, S. R., Wang, Y., & Tabien, R. E. (2015b). Mapping and validation of quantitative trait loci associated with tiller production in rice. Crop Science, 55(4), 1537–1551.

    Google Scholar 

  • Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019). Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Metabolites, 9(4), 76.

    Google Scholar 

  • Pradhan, D., Tripathy, G., & Patanaik, S. (2012). Anticancer activity of Limonia acidissima Linn (Rutaceae) fruit extracts on human breast cancer cell lines. Tropical Journal of Pharmaceutical Research, 11(3), 413–419.

    Google Scholar 

  • Prasad, L. V. (2002). Indian system of medicine and homoeopathy traditional medicine in Asia (pp. 283–286). WHO-Regional Office for South East Asia.

    Google Scholar 

  • Qian, J., Song, J., Gao, H., Zhu, Y., Xu, J., Pang, X., et al. (2013). The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PloS ONE, 8(2), e57607.

    Article  CAS  Google Scholar 

  • Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., et al. (2014). Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences, 111(14), 5135–5140.

    Article  CAS  Google Scholar 

  • Raharjo, T. J., Widjaja, I., Roytrakul, S., & Verpoorte, R. (2004). Comparative proteomics of cannabis sativa plant tissues. Journal of Biomolecular Techniques, 15, 97–106.

    Google Scholar 

  • Rastogi, S., Meena, S., & Bhattacharya, A. (2014). De novo sequencing and comparative analysis of holy and sweet basil transcrip-tomes. BMC Genomics, 15, 588–603.

    Article  Google Scholar 

  • Rastogi, S., Kalra, A., & Gupta, V. (2015). Unravelling the genome of Holy basil an incomparable“elixir of life” of traditional Indian medicine. BMC Genomics, 16, 413–431.

    Article  Google Scholar 

  • Ritchie, M. D., Holzinger, E. R., Li, R., Pendergrass, S. A., & Kim, D. (2015). Methods of integrating data to uncover genotype–phenotype interactions. Nature Reviews Genetics, 16(2), 85–97.

    Google Scholar 

  • Rubin, B. E., Ree, R. H., & Moreau, C. S. (2012). Inferring phylogenies from RAD sequence data. PLoS ONE, 7, e33394.

    Article  CAS  Google Scholar 

  • Sahu, J., Sen, P., Choudhury, M. D., Dehury, B., Barooah, M., Modi, M. K., & Talukdar, A. D. (2014). Rediscovering medicinal plants’ potential with OMICS: Microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties. OMICS: A Journal of Integrative Biology, 18(5), 298–309.

    Article  CAS  Google Scholar 

  • Saito, K., & Matsuda, F. (2010). Metabolomics for functional genomics, systems biology, and biotechnology. Annual Review of Plant Biology, 61, 463–489.

    Article  CAS  Google Scholar 

  • Salim, V., Yu, F., Altarejos, J., & De Luca, V. (2013). Virus-induced gene silencing identifies Catharanthus roseus 7-deoxyloganic acid-7- hydroxylase, a step in iridoid and monoterpene indole alkaloid biosynthesis. The Plant Journal, 76, 754–765.

    Article  CAS  Google Scholar 

  • Schmitz, R. (1985). Friedrich Wilhelm Sertürner and the discovery of morphine. Pharmacy in History, 27(2), 61–74.

    CAS  Google Scholar 

  • Seki, H., Sawai, S., Ohyama, K., Mizutani, M., Ohnishi, T., Sudo, H., et al. (2011). Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin. The Plant Cell, 23(11), 4112–4123.

    Article  CAS  Google Scholar 

  • Shi, S. G., Yang, M., Zhang, M., Wang, P., Kang, Y. X., & Liu, J. J. (2014). Genome-wide transcriptome analysis of genes involved in flavonoid biosynthesis between red and white strains of Magnolia sprengeri pamp. BMC Genomics, 15, 706–776.

    Article  Google Scholar 

  • Shivaraj, Y., Govind, S., Jogaiah, S., & Sannaningaiah, D. (2015). Functional analysis of medicinal plants using system biology approaches. International Journal of Pharmacy and Pharmaceutical Sciences, 7, 41–43.

    Google Scholar 

  • Singh, P., Guleri, R., Singh, V., Kaur, G., Kataria, H., Singh, B., Kaur, G., Kaul, S. C., Wadhwa, R., & Pati, P.K. (2015). Biotechnological interventions in Withania somnifera (L.) Dunal. Biotechnology and Genetic Engineering Reviews, 31(1–2), 1–20.

    Google Scholar 

  • Stout, J. M., Boubakir, Z., Ambrose, S. J., Purves, R. W., & Page, J. E. (2012). The hexanoyl-CoA precursor for cannabinoid biosynthesis is formed by an acyl-activating enzyme in Cannabis sativa trichomes. The Plant Journal, 71, 353–365.

    CAS  Google Scholar 

  • Suárez, A. I., & Chávez, K. (2018). Appraisal of medicinal plants with anticancer properties in South America. In M. S. Akhtar & M. K. Swamy (Eds.), Anticancer plants: properties and application (pp. 229–283). Springer.

    Chapter  Google Scholar 

  • Sumner, L. W., Lei, Z., Nikolau, B. J., & Saito, K. (2015). Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Natural Product Reports, 32(2), 212–229.

    Article  CAS  Google Scholar 

  • Sun, H., Liu, Y., Gai, Y., Geng, J., Chen, L., Liu, H., Kang, L., Tian, Y., & Li, Y. (2015). De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation. BMC Genomics, 16, 652–669.

    Article  Google Scholar 

  • Sun, X., & Weckwerth, W. (2012). COVAIN: a toolbox for uni-and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data. Metabolomics, 8(1), 81–93.

    Google Scholar 

  • Suzuki, M., Nakabayashi, R., Ogata, Y., Sakurai, N., Tokimatsu, T., Goto, S., et al. (2015). Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation. Plant Physiology, 168(1), 47–59.

    Article  CAS  Google Scholar 

  • Swamy, M. K., Paramashivaiah, S., Hiremath, L., Akhtar, M. S., & Sinniah, U. R. (2018a). Micropropagation and conservation of selected endangered anticancer medicinal plants from the Western Ghats of India. In M. S. Akhtar & M. K. Swamy (Eds.), Anticancer plants: properties and application (pp. 481–505). Springer.

    Google Scholar 

  • Swamy, M. K., Sinniah, U. R., & Ghasemzadeh, A. (2018b). Anticancer potential of rosmarinic acid and its improved production through biotechnological interventions and functional genomics. Applied Microbiology and Biotechnology, 102(18), 7775–7793.

    Article  CAS  Google Scholar 

  • Taiz, L., & Zeiger, E. (2006). Secondary metabolites and plant defense. In Plant physiology (5th ed., pp. 369–400). Sinauer Associates Inc., Publishers.

    Google Scholar 

  • Talei, D., Valdiani, A., Rafii, M. Y., & Maziah, M. (2014). Proteomic analysis of the salt-responsive leaf and root proteins in the anticancer plant Andrographis paniculata Nees. PLoS ONE, 91, e112907.

    Article  Google Scholar 

  • Talukdar, D., & Sinjushin, A. (2015). Cytogenomics and mutagenomics in plant functional biology and breeding. In PlantOmics: the omics of plant science (pp. 113–156). Springer, New Delhi.

    Google Scholar 

  • Tokimatsu, T., Sakurai, N., Suzuki, H., Ohta, H., Nishitani, K., Koyama, T., Umezawa, T., Misawa, N., Saito, K., & Shibata, D. (2005). KaPPA-View. A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiology, 138(3), 1289–1300.

    Google Scholar 

  • Tundis, R., Loizzo, M. R., & Menichini, F. (2008). Biological and pharmacological activities of Iridoids: Recent developments. Medicinal Chemistry, 8, 399–420.

    CAS  Google Scholar 

  • Upadhyay, A. K., Chacko, A. R., Gandhimathi, A., Ghosh, P., Harini, K., Joseph, A. P., Joshi, A. G., Karpe, S. D., Kaushik, S., Ku-ravadi, N., et al. (2015). Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong me-dicinal properties. BMC Plant Biology, 15, 212.

    Article  Google Scholar 

  • Urasaki, N., Takagi, H., Natsume, S., Uemura, A., Taniai, N., Miyagi, N., et al. (2017). Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Research, 24(1), 51–58.

    CAS  Google Scholar 

  • Urbanczyk‐Wochniak, E., Luedemann, A., Kopka, J., Selbig, J., Roessner‐Tunali, U., Willmitzer, L., & Fernie, A. R. (2003). Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Reports, 4(10), 989–993.

    Google Scholar 

  • Valdiani, A., Javanmard, A., Talei, D., Tan, S. G., Nikzad, S., Kadir, M. A., & Abdullah, S. N. A. (2013). Microsatellite-based evidences of genetic bottlenecks in the cryptic species “Andrographis paniculata Nees”: a potential anticancer agent. Molecular Biology Reports, 40(2), 1775–1784.

    Google Scholar 

  • Valdiani, A., Kadir, M. A., Tan, S. G., Talei, D., Abdullah, M. P., & Nikzad, S. (2012). Nain-e Havandi (Andrographis paniculata) present yesterday, absent today: A plenary review on underutilized herb of Iran’s pharmaceutical plants. Molecular Biology Reports, 39, 5409–5424.

    Article  CAS  Google Scholar 

  • Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D. A., Cestaro, A., Pruss, D., et al. (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PloS ONE, 2(12), e1326.

    Article  Google Scholar 

  • Wang, Y., Yu, R. Y., & He, Q. Y. (2015). Proteomic analysis of anticancer TCMs targeted at mitochondria. Evidence-Based Complementary and Alternative Medicine, 2015, 539260.

    Article  Google Scholar 

  • Wang, N., Wang, X., Tan, H. Y., Li, S., Tsang, C. M., Tsao, S. W., & Feng, Y. (2016). Berberine suppresses cyclin D1 expression through proteasomal degradation in human hepatoma cells. International Journal of Molecular Sciences, 17, 1899.

    Article  Google Scholar 

  • Weckwerth, W. (2011). Green systems biology—from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. Journal of Proteomics, 75(1), 284–305.

    Google Scholar 

  • Weckwerth, W. (2019) Toward a unification of system-theoretical principles in biology and ecology—the stochastic lyapunov matrix equation and its inverse application. Frontiers in Applied Mathematics and Statistics, 5, 29

    Google Scholar 

  • Weckwerth, W., Ghatak, A., Bellaire, A., Chaturvedi, P., & Varshney, R. K. (2020). PANOMICS meets germplasm. Plant Biotechnology Journal, 18(7), 1507–1525.

    Google Scholar 

  • Wen, W., Li, D., Li, X., Gao, Y., Li, W., Li, H., Liu, J., Liu, H., Chen, W., Luo, J. and Yan, J., 2014. Metabolomebased genome-wide association study of maize kernel leads to novel biochemical insights. Nature Communications, 5(1), 1–10.

    Google Scholar 

  • Wenping, H., Yuan, Z., Jie, S., Lijun, Z., & Zhezhi, W. (2011). De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients. Genomics, 98, 272–279.

    Article  Google Scholar 

  • Winzer, T., Gazda, V., He, Z., Kaminski, F., Kern, M., Larson, T. R., et al. (2012). A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science, 336(6089), 1704–1708.

    Article  CAS  Google Scholar 

  • World Health Organization. (2015). Connecting global priorities: biodiversity and human health. World Health Organization and Secretariat of the Convention on Biological Diversity.

    Google Scholar 

  • Wurtele, E. S., Chappell, J., Jones, A. D., Celiz, M. D., Ransom, N., Hur, M., et al. (2012). Medicinal plants: a public resource for metabolomics and hypothesis development. Metabolites, 2(4), 1031–1059.

    Article  CAS  Google Scholar 

  • Xie, G., Plumb, R., Su, M., Xu, Z., Zhao, A., Qiu, M., Long, X., Liu, Z., & Jia, W. (2008). Ultra-performance LC/TOF MS analysis of medicinal Panax herbs for metabolomic research. Journal of Separation Science, 31, 1015–1026.

    Article  CAS  Google Scholar 

  • Xu, H., Song, J., Luo, H., Zhang, Y., Li, Q., Zhu, Y., Xu, J., Li, Y., Song, C., Wang, B., et al. (2016). Analysis 26 of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza. Molecular Plant, 9, 949–952.

    Article  CAS  Google Scholar 

  • Yamada, T., Matsuda, F., Kasai, K., Fukuoka, S., Kitamura, K., Tozawa, Y., Miyagawa, H., & Wakasa, K. (2008). Mutation of a rice gene encoding a phenylalanine biosynthetic enzyme results in accumulation of phenylalanine and tryptophan. Plant Cell, 20, 1316–1329.

    Article  CAS  Google Scholar 

  • Yamazaki, M., Mochida, K., Asano, T., Nakabayashi, R., Chiba, M., Udomson, N., Yamazaki, Y., Goodenowe, D. B., Sankawa, U., Yoshida, T., et al. (2013). Coupling deep transcriptome analysis with untargeted metabolic profiling in Ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones. Plant and Cell Physiology, 54(5), 686–696.

    Article  CAS  Google Scholar 

  • Yan, L., Wang, X., Liu, H., Tian, Y., Lian, J., Yang, R., & Sheng, J. (2015). The genome of Dendrobium officinale illuminates the biology of the important traditional Chinese orchid herb. Molecular Plant, 8(6), 922–934.

    Article  CAS  Google Scholar 

  • Yang, W., Guo, Z., Huang, C., Duan, L., Chen, G., Jiang, N., Fang, W., Feng, H., Xie, W., Lian, X., et al. (2014). Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nature Communications, 5, 5087.

    Article  CAS  Google Scholar 

  • Yang, Y., Moore, M. J., Brockington, S. F., Soltis, D. E., Wong, G. K., Carpenter, E. J., Zhang, Y., Chen, L., Yan, Z., & Xie, Y. (2015). Dissecting molecular evolution in the highly diverse plant clade Caryo-phyllales using transcriptome sequencing. Molecular Biology and Evolution, 32, 2001–2014.

    Article  CAS  Google Scholar 

  • Yonekura-Sakakibara, K., Fukushima, A., & Saito, K. (2013). Transcriptome data modeling for targeted plant metabolic engineering. Current Opinion in Biotechnology, 24(2), 285–290.

    Article  CAS  Google Scholar 

  • Zhang, A., Sun, H., Yuan, Y., Sun, W., Jiao, G., & Wang, X. (2011). An in vivo analysis of the therapeutic and synergistic properties of Chinese medicinal formula Yin-Chen-Hao-Tang based on its active constituents. Fitoterapia, 82, 1160–1168.

    Article  CAS  Google Scholar 

  • Zhang, T., Shao, M. F., & Ye, L. (2012). 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. The ISME Journal, 6(6), 1137–1147.

    Google Scholar 

  • Zhang, F., Gao, Q., Khan, G., Luo, K., & Chen, S. (2014). Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau. Gene, 553, 90–97.

    Article  CAS  Google Scholar 

  • Zhang, X., Huang, C., Wu, D., Qiao, F., Li, W., Duan, L., ... & Yan, J. (2017). High-throughput phenotyping and QTL mapping reveals the genetic architecture of maize plant growth. Plant Physiology, 173(3), 1554–1564.

    Google Scholar 

  • Zhao, B., Luo, T., Li, T., Li, Y., Zhang, J., Shan, Y., Wang, X., Yang, L., Zhou, F., Zhu, Z., & Zhu, H. (2019). Genome-wide association analysis of 19,629 individuals identifies variants influencing regional brain volumes and refines their genetic co-architecture with cognitive and mental health traits. Nature Genetics, 51(11), 1637–1644.

    Google Scholar 

  • Zhao, Y., Yin, J., Guo, H., Zhang, Y., Xiao, W., Sun, C., Wu, J., Qu, X., Yu, J., Wang, X., et al. (2015). The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Frontiers in Plant Science, 5, 696.

    Article  Google Scholar 

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Younas, A., Riaz, N., Rashid, M. (2023). Multi-Omics Approaches for Breeding in Medicinal Plants. In: Prakash, C.S., Fiaz, S., Nadeem, M.A., Baloch, F.S., Qayyum, A. (eds) Sustainable Agriculture in the Era of the OMICs Revolution. Springer, Cham. https://doi.org/10.1007/978-3-031-15568-0_8

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