Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Abstract

Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.

References

[1] Zaynab M, Fatima M, Abbas S et al. Role of secondary metabolites in plant defense against pathogens. Microb Pathog. 2018; 124: 198-202.

[2] Adedeji AA, Babalola OO . Secondary metabolites as plant defensive strategy: a large role for small molecules in the near root region. Planta. 2020; 252: 61.

[3] Li YQ, Kong D, Fu Y et al. The effect of developmental and environmental factors on secondary metabolites in medicinal plants. Plant Physiol Biochem. 2020; 148: 80-9.

[4] Yang L, Wen KS, Ruan X et al. Response of plant secondary metabolites to environmental factors. Molecules. 2018; 23: 762.

[5] Wang SC, Alseekh S, Fernie AR et al. The structure and function of major plant metabolite modifications. Mol Plant. 2019; 12: 899-919.

[6] Marchiosi R, dos Santos WD, Constantin RP et al. Biosynthesis and metabolic actions of simple phenolic acids in plants. Phytochem Rev. 2020; 19: 865-906.

[7] Koeduka T. The phenylpropene synthase pathway and its applications in the engineering of volatile phenylpropanoids in plants. Plant Biotechnol (Tokyo). 2014; 31: 401-7.

[8] Ye P, Liang S, Wang X et al. Transcriptome analysis and targeted metabolic profiling for pathway elucidation and identification of a geraniol synthase involved in iridoid biosynthesis from Gardenia jasminoides. Ind Crop Prod. 2019; 132: 48-58.

[9] Šantić Ž et al. The historical use of medicinal plants in traditional and scientific medicine. Psychiatr Danub. 2017; 4: 787-92.

[10] Lietava J et al. Medicinal plants in a middle Paleolithic grave Shanidar IV? J Ethnopharmacol. 1992; 35: 263-6.

[11] Norn S, Kruse PR, Kruse E . History of opium poppy and morphine. Dan Medicinhist Arbog. 2005; 33: 171-84.

[12] Sanchez-Ramos JR et al. The rise and fall of tobacco as a botanical medicine. J Herb Med. 2020; 22: 100374.

[13] Warner KE, MacKay J . The global tobacco disease pandemic: nature, causes, and cures. Glob Public Health. 2006; 1: 65-86.

[14] Jurna I . Serturner und Morphin? Eine historische vignette. Schmerz. 2003; 17: 280-3.

[15] Achan J, Talisuna AO, Erhart A et al. Quinine, an old antimalarial drug in a modern world: role in the treatment of malaria. Malar J. 2011; 10: 144.

[16] Desborough MJR, Keeling DM . The aspirin story - from willow to wonder drug. Br J Haematol. 2017; 177: 674-83.

[17] World Health Organization . World Malaria Report 2010 . Geneva: WHO; 2010.

[18] Weaver BA . How taxol/paclitaxel kills cancer cells. Mol Biol Cell. 2014; 25: 2677-81.

[19] Barnette KG, Gordon MS, Rodriguez D et al. Oral sabizabulin for high-risk, hospitalized adults with Covid-19: interim analysis. NEJM Evid. 2022; 1: EVIDoa2200145.

[20] Jorgensen SCJ, Kebriaei R, Dresser LD . Remdesivir: review of pharmacology, pre-clinical data, and emerging clinical experience for COVID-19. Pharmacotherapy 2020; 40: 659-71.

[21] Mitjà O, Clotet B . Use of antiviral drugs to reduce COVID-19 transmission. Lancet Glob Health 2020; 8: e639-40.

[22] Wu CR, Liu Y, Yang Y et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020; 10: 766-88.

[23] Liang SJ et al. Study on flavonoid and bioactivity features of the pericarp of Citri Reticulatae ‘Chachi’ during storage. Arab J Chem. 2021; 15: 103653.

[24] Hu K, Guan WJ, Bi Y et al. Efficacy and safety of Lianhuaqingwen capsules, a repurposed Chinese herb, in patients with coronavirus disease 2019: a multicenter, prospective, randomized controlled trial. Phytomedicine. 2021; 85: 153242.

[25] Lichman BR . The scaffold-forming steps of plant alkaloid biosynthesis. Nat Pro Rep. 2021; 38: 103-29.

[26] Yang CQ, Fang X, Wu XM et al. Transcriptional regulation of plant secondary MetabolismF. J Integr Plant Biol. 2012; 54: 703-12.

[27] Beniddir MAB, Kang KB, Genta-Jouve G et al. Advances in decomposing complex metabolite mixtures using substructure-and network-based computational metabolomics approaches. Nat Prod Rep. 2021; 38: 1967-93.

[28] Bohlmann J, Meyer-Gauen G, Croteau R . Plant terpenoid synthases: molecular biology and phylogenetic analysis. PNAS. 1998; 95: 4126-33.

[29] Attieh J, Djiana R, Koonjul P et al. Cloning and functional expression of two plant thiol ethyltransferases: a new class of enzymes involved in the biosynthesis of sulfur volatiles. Plant Mol Biol. 2002; 50: 511-21.

[30] Ounaroon A, Decker G, Schmidt J et al. (R, S)-Reticuline 7-O-methyltransferase and (R, S)-norcoclaurine 6-O-methyltransferase of Papaver somniferum - cDNA cloning and characterization of methyl transfer enzymes of alkaloid biosynthesis in opium poppy. Plant J. 2003; 36: 808-19.

[31] Isabel DP . Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures. BMC Plant Biol. 2010; 10: 252.

[32] Zeng JG, Liu Y, Liu W et al. Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa. PLoS One. 2013; 8: e53409.

[33] Kellner F, Kim J, Clavijo BJ et al. Genome-guided investigation of plant natural product biosynthesis. Plant J. 2015; 82: 680-92.

[34] Nett RS, Lau W, Sattely ES . Discovery and engineering of colchicine alkaloid biosynthesis. Nature. 2020; 584: 148-53.

[35] Hong B, Grzech D, Caputi L et al. Biosynthesis of strychnine. Nature. 2022; 607: 617-22.

[36] Ajikumar PK, Xiao WH, Tyo KEJ et al. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science. 2010; 330: 70-4.

[37] Kitade Y et al. Production of 4-hydroxybenzoic acid by an aerobic growth-arrested bioprocess using metabolically engineered Corynebacterium glutamicum. Appl Environ Microbiol. 2018; 84: e02587-17.

[38] Galanie S, Thodey K, Trenchard IJ et al. Complete biosynthesis of opioids in yeast. Science. 2015; 349: 1095-100.

[39] Wriessnegger T, Augustin P, Engleder M et al. Production of the sesquiterpenoid (+)-nootkatone by metabolic engineering of Pichia pastoris. Metab Eng. 2014; 24: 18-29.

[40] Schultz BJ, Kim SY, Lau W et al. Total biosynthesis for milligram-scale production of etoposide intermediates in a plant chassis. J Am Chem Soc. 2019; 141: 19231-5.

[41] Cordero BF, Couso I, León R et al. Enhancement of carotenoids biosynthesis in Chlamydomonas reinhardtii by nuclear transformation using a phytoene synthase gene isolated from chlorella zofingiensis. Appl Microbio Biotech. 2011; 91: 341-51.

[42] Xue J, Niu YF, Huang T et al. Genetic improvement of the microalga Phaeodactylum tricornutum for boosting neutral lipid accumulation. Metab Eng. 2015; 27: 1-9.

[43] Wang R, Shu P, Zhang C et al. Integrative analyses of metabolome and genome-wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit (Actinidia chinensis). New Phytol. 2022; 233: 373-89.

[44] Li Y, Chen Y, Zhou L et al. Microtom metabolic network: rewiring tomato metabolic regulatory network throughout the growth cycle. Mol Plant. 2020; 13: 1203-18.

[45] Yang C, Shen S, Zhou S et al. Rice metabolic regulatory network spanning the entire life cycle. Mol Plant. 2022; 15: 258-75.

[46] Chen F, Song Y, Li X et al. Genome sequences of horticultural plants: past, present, and future. Hortic Res. 2019; 6: 112.

[47] Liao B, Hu H, Xiao S et al. Global pharmacopoeia genome database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. Sci China Life Sci. 2022; 65: 809-17.

[48] Chen S et al. Strategies of the study on herb genome program. Acta Pharm Sin B. 2010; 45: 807-12.

[49] Guo L, Winzer T, Yang X et al. The opium poppy genome and morphinan production. Science. 2018; 362: 343-7.

[50] Kang M et al. A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis. Nat Commun. 2021; 12: 1-12.

[51] Zhao Q, Yang J, Cui MY et al. The reference genome sequence of Scutellaria baicalensis provides insights into the evolution of wogonin biosynthesis. Mol Plant. 2019; 12: 935-50.

[52] Jiang Z, Tu L, Yang W et al. The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis. Plant Commun. 2021; 2: 100113.

[53] Tu L, Ping S, Zhang Z et al. Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis. Nat Commun. 2020; 11: 1-12.

[54] Song Z, Lin C, Xing P et al. A highquality reference genome sequence of salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes. Plant Genome. 2020; 13: e20041.

[55] Cheng J, Wang X, Liu X et al. Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway. Mol Plant. 2021; 14: 1199-209.

[56] He S, Dong X, Zhang G et al. High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. Mol Ecol Resour. 2021; 21: 153-69.

[57] Yang X, Gao S, Guo L et al. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nat Commun. 2021; 12: 6030.

[58] Caputi L, Franke J, Farrow SC et al. Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle. Science. 2018; 360: 1235-9.

[59] Fan G, Liu X, Sun S et al. The chromosome level genome and genome-wide association study for the agronomic traits of Panax Notoginseng. iScience. 2020; 23: 101538.

[60] Song X, Sun P, Yuan J et al. The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales. Plant Biotechnol J. 2021; 19: 731-44.

[61] Wang Y et al. Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. Nat Commun. 2022; 13: 1-16.

[62] Song X, Wang J, Li N et al. Deciphering the high-quality genome sequence of coriander that causes controversial feelings. Plant Biotechnol J. 2020; 18: 1444-56.

[63] Wang Z et al. Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. Nat Commun. 2022; 13: 1-12.

[64] Sun X, Zhu S, Li N et al. A chromosome-level genome assembly of garlic (Allium sativum) provides insights into genome evolution and allicin biosynthesis. Mol Plant. 2020; 13: 1328-39.

[65] Han B, Jing Y, Dai J et al. A chromosome-level genome assembly of dendrobium huoshanense using long reads and hi-C data. Genome Biol Evol. 2020; 12: 2486-90.

[66] Niu Z, Zhu F, Fan Y et al. The chromosome-level reference genome assembly for Dendrobium officinale and its utility of functional genomics research and molecular breeding study. Acta Pharm Sin B. 2021; 11: 2080-92.

[67] Bae E, An C, Kang MJ et al. Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. G3. 2022; 12: jkab433.

[68] Fan W, Wang S, Wang H et al. The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo-polyploidization history and plant inulin production. Mol Ecol Resour. 2022; 22: 3124-40.

[69] Liao B, Shen X, Xiang L et al. Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield. Mol Plant. 2022; 15: 1310-28.

[70] Miao Y, Luo D, Zhao T et al. Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi. Plant Biotechnol J. 2022; 20: 1902-15.

[71] Wu Z, Liu H, Zhan W et al. The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis. Plant Biotechnol J. 2021; 19: 1725-42.

[72] Song C, Liu Y, Song A et al. The chrysanthemum nankingense genome provides insights into the evolution and diversification of chrysanthemum flowers and medicinal traits. Mol Plant. 2018; 11: 1482-91.

[73] Jia Y, Chen S, Chen W et al. A chromosome-level reference genome of Chinese balloon flower (Platycodon grandiflorus). Front Genet. 2022; 13: 869784.

[74] Kang M, Wu H, Yang Q et al. A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine. Hortic Res. 2020; 7: 18.

[75] Zhang J, Tian Y, Yan L et al. Genome of plant maca (Lepidium meyenii) illuminates genomic basis for high-altitude adaptation in the Central Andes. Mol Plant. 2016; 9: 1066-77.

[76] Li C et al. Assembly and annotation of a draft genome of the medicinal plant Polygonum cuspidatum. Front Plant Sci. 2019; 10: 1274.

[77] Yang Y, Sun P, Lv L et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat Plants. 2020; 6: 215-22.

[78] Xie D, Xu Y, Wang J et al. The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. Nat Commun. 2019; 10: 5158.

[79] Huang D, Ming R, Xu S et al. Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis. DNA Res. 2021; 28: dsab018.

[80] Wu H, Zhao G, Gong H et al. A high-quality sponge gourd (Luffa cylindrica) genome. Hortic Res. 2020; 7: 128.

[81] Cui J, Yang Y, Luo S et al. Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.). Hortic Res. 2020; 7: 85.

[82] Xia M et al. Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo. Gigascience. 2018; 7: giy067.

[83] Pu X, Li Z, Tian Y et al. The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. New Phytol. 2020; 227: 930-43.

[84] Akagi T, Shirasawa K, Nagasaki H et al. The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet. 2020; 16: e1008566.

[85] Xia E, Zhang HB, Sheng J et al. The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant. 2017; 10: 866-77.

[86] Mochida K, Sakurai T, Seki H et al. Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J. 2017; 89: 181-94.

[87] Kang S et al. Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. Nat Commun. 2020; 11: 1-11.

[88] Qin S, Wu L, Wei K et al. A draft genome for Spatholobus suberectus. Sci Data. 2019; 6: 1-9.

[89] Li Y, Wei H, Yang J et al. High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis. Hortic Res. 2020; 7: 183.

[90] Hoopes GM, Hamilton JP, Kim J et al. Genome assembly and annotation of the medicinal PlantCalotropis gigantea, a producer of anticancer and antimalarial cardenolides. G3. 2018; 8: 385-91.

[91] Liu Y, Tang Q, Cheng P et al. Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans. Acta Pharm Sin B. 2020; 10: 374-82.

[92] Xu Z et al. Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants. BMC Biol. 2020; 18: 1-14.

[93] Wang J, Xu S, Mei Y et al. A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China. Hortic Res. 2021; 8: 135.

[94] Rai A et al. Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun. 2021; 12: 1-19.

[95] Liang Y, Chen S, Wei K et al. Chromosome level genome assembly of Andrographis paniculata. Front Genet. 2020; 11: 701.

[96] Vining KJ, Johnson SR, Ahkami A et al. Draft genome sequence of Mentha longifolia and development of resources for mint cultivar improvement. Mol Plant. 2017; 10: 323-39.

[97] Bornowski N, Hamilton JP, Liao P et al. Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae. DNA Res. 2020; 27: dsaa016.

[98] Zhang Y et al. Incipient diploidization of the medicinal plant Perilla within 10,000 years. Nat Commun. 2021; 12: 1-13.

[99] Shen Y, Li W, Zeng Y et al. Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli. Nat Commun. 2022; 13: 1-15.

[100] Zheng X, Chen D, Chen B et al. Insights into salvianolic acid B biosynthesis from chromosome-scale assembly of the salvia bowleyana genome. Acta Bot Sin. 2021; 63: 1309-23.

[101] Jia K, Liu H, Zhang RG et al. Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. Hortic Res. 2021; 8: 177.

[102] Xu Z, Gao R, Pu X et al. Comparative genome analysis of Scutellaria baicalensis and Scutellaria barbata reveals the evolution of active flavonoid biosynthesis. Genom Proteom Bioinform 2020; 18: 230-40.

[103] Li L, Cushman SA, He YX et al. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. Hortic Res. 2020; 7: 130.

[104] Li M, Zhang D, Gao Q et al. Genome structure and evolution of Antirrhinum majus L. Nat Plants. 2019; 5: 174-83.

[105] Shang J et al. The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter. Genome Biol. 2020; 21: 1-28.

[106] Chaw SM, Liu YC, Wu YW et al. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nat Plants. 2019; 5: 63-73.

[107] Li J, Lv M, Du L et al. An enormous Paris polyphylla genome sheds light on genome size evolution and polyphyllin biogenesis. BioRxiv 2020. preprint: not peer reviewed.

[108] Chan AP, Crabtree J, Zhao Q et al. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol. 2010; 28: 951-6.

[109] Zhou W et al. Whole-genome sequence data of Hypericum perforatum and functional characterization of melatonin biosynthesis by N-acetylserotonin O-methyltransferase. J Pineal Res. 2021; 70: e12709.

[110] Wang Z, Hobson N, Galindo L et al. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J. 2012; 72: 461-73.

[111] Xia Z, Huang D, Zhang S et al. Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims). Hortic Res. 2021; 8: 14.

[112] Nong W, Law STS, Wong AYP et al. Chromosomal-level reference genome of the incense tree Aquilaria sinensis. Mol Ecol Resour. 2020; 20: 971-9.

[113] Qin G, Xu C, Ming R et al. The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis. Plant J. 2017; 91: 1108-28.

[114] Zhang L, Chen F, Zhang X et al. The water lily genome and the early evolution of flowering plants. Nature. 2020; 577: 79-84.

[115] Cui X, Meng F, Pan X et al. Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids. Hortic Res. 2022; 9: uhac005.

[116] Hu L, Xu Z, Wang M et al. The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat Commun. 2019; 10: 4702.

[117] Guo C, Wang Y, Yang A et al. The Coix genome provides insights into Panicoideae evolution and papery hull domestication. Mol Plant. 2020; 13: 309-20.

[118] Shi T, Rahmani RS, Gugger PF et al. Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Mol Biol Evol. 2020; 37: 2394-413.

[119] Liu X, Liu Y, Huang P et al. The genome of medicinal plant Macleaya cordata provides new insights into benzylisoquinoline alkaloids metabolism. Mol Plant. 2017; 10: 975-89.

[120] Liu Y et al. Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nat Commun. 2021; 12: 1-13.

[121] Grassa CJ, Wenger JP, Dabney C et al. A complete cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content. New Phytol. 2021; 230: 1665-79.

[122] Peng X, Liu H, Chen P et al. A chromosome-scale genome assembly of paper mulberry (Broussonetia papyrifera) provides new insights into its forage and papermaking usage. Mol Plant. 2019; 12: 661-77.

[123] Xuan Y, Ma B, Li D et al. Chromosome restructuring and number change during the evolution of Morus notabilis and Morus alba. Hortic Res. 2022; 9: uhab030.

[124] Liu M, Zhao J, Cai QL et al. The complex jujube genome provides insights into fruit tree biology. Nat Commun. 2014; 5: 5315.

[125] Jiang S, An H, Xu F et al. Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome. GigaScience. 2020; 9: giaa015.

[126] Raymond O, Gouzy J, Just J et al. The Rosa genome provides new insights into the domestication of modern roses. Nat Genet. 2018; 50: 772-7.

[127] Luan M, Jian JB, Chen P et al. Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich. Mol Eco Resour. 2018; 18: 639-45.

[128] Zeng L, Tu XL, Dai H et al. Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol. 2019; 20: 79.

[129] Ma Q, Sun T, Li S et al. The Acer truncatum genome provides insights into nervonic acid biosynthesis. Plant J. 2020; 104: 662-78.

[130] Liang Q, Li H, Li S et al. The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge). GigaScience. 2019; 8: giz071.

[131] Fu Y, Li L, Hao S et al. Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. Gigascience. 2017; 6: 1-5.

[132] Hoshino A, Jayakumar V, Nitasaka E et al. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun. 2016; 7: 13295.

[133] De-la-Cruz IM, Hallab A, Olivares-Pinto U et al. Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). Sci Rep. 2021; 11: 882.

[134] Yang P, Zhao HY, Wei JS et al. Chromosome-level genome assembly and functional characterization of terpene synthases provide insights into the volatile terpenoid biosynthesis of Wurfbainia villosa. Plant J. 2022.

[135] Li H, Wu L, Dong Z et al. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. Hortic Res. 2021; 8: 189.

[136] Xu Z, Xin T, Bartels D et al. Genome analysis of the ancient tracheophyte Selaginella tamariscina reveals evolutionary features relevant to the acquisition of desiccation tolerance. Mol Plant. 2018; 11: 983-94.

[137] Liu H, Wang X, Wang G et al. The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nat Plants. 2021; 7: 748-56.

[138] Wan T, Liu ZM, Li LF et al. A genome for gnetophytes and early evolution of seed plants. Nat Plants. 2018; 4: 82-9.

[139] Xiong X, Gou J, Liao Q et al. The Taxus genome provides insights into paclitaxel biosynthesis. Nat Plants. 2021; 7: 1026-36.

[140] Field B, Osbourn AE . Metabolic diversification-independent assembly of operon-like gene clusters in different plants. Science. 2008; 320: 543-7.

[141] Field B, Fiston-Lavier AS, Kemen A et al. Formation of plant metabolic gene clusters within dynamic chromosomal regions. PNAS. 2011; 108: 16116-21.

[142] Mao LF, Kawaide H, Higuchi T et al. Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. PNAS. 2020; 117: 12472-80.

[143] Frey M, Chomet P, Glawischnig E et al. Analysis of a chemical plant defense mechanism in grasses. Science. 1997; 277: 696-9.

[144] Itkin M, Heinig U, Tzfadia O et al. Biosynthesis of antinutritional alkaloids in Solanaceous crops is mediated by clustered genes. Science. 2013; 341: 175-9.

[145] Jeon JE, Kim JG, Fischer CR et al. A pathogen-responsive gene cluster for highly modified fatty acids in tomato. Cell. 2020; 180: 176-187.e19.

[146] Kautsar SA, Suarez Duran HG, Blin K et al. PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res. 2017; 45: W55-63.

[147] Töpfer N, Fuchs LM, Aharoni A . The PhytoClust tool for metabolic gene clusters discovery in plant genomes. Nucleic Acids Res. 2017; 45: 7049-63.

[148] Schläpfer P, Zhang P, Wang C et al. Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiol. 2017; 173: 2041-59.

[149] Winzer T, Gazda V, He Z et al. A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine. Science. 2012; 336: 1704-8.

[150] Matsuba Y, Zi J, Jones AD et al. Biosynthesis of the diterpenoid lycosantalonol via nerylneryl diphosphate in Solanum lycopersicum. PLoS One. 2015; 10: e0119302.

[151] Kong D, Li S, Smolke CD . Discovery of a previously unknown biosynthetic capacity of naringenin chalcone synthase by heterologous expression of a tomato gene cluster in yeast. Sci Adv. 2020; 6: eabd1143.

[152] Polturak G, Dippe M, Stephenson MJ et al. Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat. PNAS. 2022; 119: e2123299119.

[153] Wu D, Jiang B, Ye CY et al. Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants. Plant Commun. 2022; 3: 100320.

[154] Ma J, Wang S, Zhu X et al. Major episodes of horizontal gene transfer drove the evolution of land plants. Mol Plant. 2022; 15: 857-71.

[155] Fan P, Wang P, Lou YR et al. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. elife. 2020; 9: e56717.

[156] Kotopka BJ, Smolke CD . Production of the cyanogenic glycoside dhurrin in yeast. Metab Eng Commun. 2019; 9: e00092.

[157] Clevenger KD, Bok JW, Ye R et al. A scalable platform to identify fungal secondary metabolites and their gene clusters. Nat Chem Biol. 2017; 13: 895-901.

[158] Li Q, Ramasamy S, Singh P et al. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy. Nat Commun. 2020; 11: 190.

[159] Wetzstein HY, Porter JA, Janick J et al. Selection and clonal propagation of high artemisinin genotypes of Artemisia annua. Front Plant Sci. 2018; 9: 358.

[160] Graham IA, Besser K, Blumer S et al. The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. Science. 2010; 327: 328-31.

[161] Celik I, Camci H, Kose A et al. Molecular genetic diversity and association mapping of morphine content and agronomic traits in Turkish opium poppy (Papaver somniferum) germplasm. Mol Breeding. 2016; 36: 46.

[162] Naim-Feil E et al. The characterization of key physiological traits of medicinal cannabis (Cannabis sativa L.) as a tool for precision breeding. BMC Plant Biol. 2021; 21: 1-15.

[163] Westfall PJ, Pitera DJ, Lenihan JR et al. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. PNAS. 2012; 109: E111-8.

[164] Gao CX . Genome engineering for crop improvement and future agriculture. Cell. 2021; 184: 1621-35.

[165] Alagoz Y et al. Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci Rep. 2016; 6: 1-9.

[166] Li B, Cui G, Shen G et al. Targeted mutagenesis in the medicinal plant salvia miltiorrhiza. Sci Rep. 2017; 7: 1-9.

[167] Kui L, Chen H, Zhang W et al. Building a genetic manipulation tool box for orchid biology: identification of constitutive promoters and application of CRISPR/Cas9 in the orchid, Dendrobium officinale. Front Plant Sci. 2017; 7: 2036.

[168] Jiang WZ, Henry IM, Lynagh PG et al. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnol J. 2017; 15: 648-57.

[169] Zhu X, Liu X, Liu T et al. Synthetic biology of plant natural products: from pathway elucidation to engineered biosynthesis in plant cells. Plant Commun. 2021; 2: 100229.

[170] Ye XD, al-Babili S, Klöti A et al. Engineering the provitamin a (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science. 2000; 287: 303-5.

[171] Zhu Q, Yu S, Zeng D et al. Development of “purple endosperm rice” by engineering anthocyanin biosynthesis in the endosperm with a high-efficiency transgene stacking system. Mol Plant. 2017; 10: 918-29.

[172] Zhu C, Naqvi S, Breitenbach J et al. Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize. PNAS. 2008; 105: 18232-7.

[173] Fuentes P, Zhou F, Erban A et al. A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop. elife. 2016; 5: e13664.

[174] De La Peña R, Sattely ES . Rerouting plant terpene biosynthesis enables momilactone pathway elucidation. Nat Chem Biol. 2021; 17: 205-12.

[175] Li J, Mutanda I, Wang K et al. Chloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana. Nat Commun. 2019; 10: 4850.

[176] Farag S, Kayser O . Cannabinoids production by hairy root cultures of Cannabis sativa L. J Plant Sci USA. 2015; 6: 1874-84.

[177] Kim YK, Kim YB, Uddin MR et al. Enhanced triterpene accumulation in Panax ginseng hairy roots overexpressing mevalonate-5-pyrophosphate decarboxylase and farnesyl pyrophosphate synthase. ACS Synth Biol. 2014; 3: 773-9.

[178] Singh S, Pandey P, Akhtar MQ et al. A new synthetic biology approach for the production of curcumin and its glucoside in Atropa belladonna hairy roots. J Biotechnol. 2021; 328: 23-33.

[179] Martínez-Márquez A, Morante-Carriel JA, Ramírez-Estrada K et al. Production of highly bioactive resveratrol analogues pterostilbene and piceatannol in metabolically engineered grapevine cell cultures. Plant Biotechnol J. 2016; 14: 1813-25.

[180] Schuurink R, Tissier A . Glandular trichomes: micro-organs with model status? New Phytol. 2020; 225: 2251-66.

[181] Kortbeek RW, Xu J, Ramirez A et al. Engineering of tomato glandular trichomes for the production of specialized metabolites. Method Enzymol. 2016; 576: 305-31.

[182] Xu X, Liu Y, Du G et al. Microbial chassis development for natural product biosynthesis. Trends Biotechnol. 2020; 38: 779-96.

[183] Paddon CJ, Westfall PJ, Pitera DJ et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature. 2013; 496: 528-32.

[184] Luo X, Reiter MA, d’Espaux L et al. Complete biosynthesis of cannabinoids and their unnatural analogues in yeast. Nature. 2019; 567: 123-6.

[185] Li Y, Li S, Thodey K et al. Complete biosynthesis of noscapine and halogenated alkaloids in yeast. PNAS. 2018; 115: E3922-31.

[186] Tsuruta H, Paddon CJ, Eng D et al. High-level production of amorpha-4, 11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One. 2009; 4: e4489.

[187] Osorio-Montalvo P, Sáenz-Carbonell L, de-la-Peña C . 5-Azacytidine: a promoter of epigenetic changes in the quest to improve plant somatic embryogenesis. Int J Mol Sci. 2018; 19: 3182.

[188] Zhao C, Liu X, Gong Q et al. Three AP2/ERF family members modulate flavonoid synthesis by regulating type IV chalcone isomerase in citrus. Plant Biotechnol J. 2021; 19: 671-88.

[189] Goodrich J, Carpenter R, Coen ES . A common gene regulates pigmentation pattern in diverse plant species. Cell. 1992; 68: 955-64.

[190] Nakatsuka T, Haruta KS, Pitaksutheepong C et al. Identification and characterization of R2R3-MYB and bHLH transcription factors regulating anthocyanin biosynthesis in gentian flowers. Plant Cell Physiol. 2008; 49: 1818-29.

[191] Spelt C, Quattrocchio F, Mol JNM et al. anthocyanin1of petunia encodes a basic helix-loop-helix protein that directly activates transcription of structural anthocyanin genes. Plant Cell. 2000; 12: 1619-31.

[192] Liu X, Yin XR, Allan AC et al. The role of MrbHLH1 and MrMYB1 in regulating anthocyanin biosynthetic genes in tobacco and Chinese bayberry (Myrica rubra) during anthocyanin biosynthesis. Plant Cell Tiss Org. 2013; 115: 285-98.

[193] Huang W et al. A R2R3-MYB transcription factor regulates the flavonol biosynthetic pathway in a traditional Chinese medicinal plant, Epimedium sagittatum. Front Plant Sci. 2016; 7: 1089.

[194] Liu C, Long J, Zhu K et al. Characterization of a citrus R2R3-MYB transcription factor that regulates the flavonol and hydroxycinnamic acid biosynthesis. Sci Rep. 2016; 26: 2535.

[195] Xu F, Ning Y, Zhang W et al. An R2R3-MYB transcription factor as a negative regulator of the flavonoid biosynthesis pathway in Ginkgo biloba. Funct Integr Genomics. 2014; 14: 177-89.

[196] Sablowski RW, Moyano E, Culianez-Macia FA et al. A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes. EMBO J. 1994; 13: 128-37.

[197] Moyano E, Martínez-Garcia JF, Martin C . Apparent redundancy in myb gene function provides gearing for the control of flavonoid biosynthesis in antirrhinum flowers. Plant Cell. 1996; 8: 1519-32.

[198] Schwinn K, Venail J, Shang Y et al. A small family of MYB-regulatory genes controls floral pigmentation intensity and patterning in the genus antirrhinum. Plant Cell. 2006; 18: 831-51.

[199] Morita Y, Saitoh M, Hoshino A et al. Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and ca mutations conferring white flowers in the Japanese morning glory. Plant Cell Physiol. 2006; 47: 457-70.

[200] Pang Y, Wenger JP, Saathoff K et al. A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development. Plant Physiol. 2009; 151: 1114-29.

[201] Yu ZX, Li JX, Yang CQ et al. The jasmonate-responsive AP2/ERF transcription factors AaERF1 and AaERF2 positively regulate artemisinin biosynthesis in Artemisia annua L. Mol Plant. 2012; 5: 353-65.

[202] Lu X, Zhang L, Zhang F et al. AaORA, a trichome-specific AP2/ERF transcription factor of Artemisia annua, is a positive regulator in the artemisinin biosynthetic pathway and in disease resistance to Botrytis cinerea. New Phytol. 2013; 198: 1191-202.

[203] Tan H, Xiao L, Gao S et al. Trichome and artemisinin regulator 1 is required for trichome development and artemisinin biosynthesis in Artemisia annua. Mol Plant. 2015; 8: 1396-411.

[204] Zhang J et al. Expression analysis of transcription factor ERF gene family of Panax ginseng. China J Chin Mater Med. 2020; 45: 2515-22.

[205] Zhang F, Fu X, Lv Z et al. A basic leucine zipper transcription factor, AabZIP1, connects abscisic acid signaling with artemisinin biosynthesis in Artemisia annua. Mol Plant. 2015; 8: 163-75.

[206] Ma D, Pu G, Lei C et al. Isolation and characterization of AaWRKY1, an Artemisia annua transcription factor that regulates the amorpha-4,11-diene synthase gene, a key gene of artemisinin biosynthesis. Plant Cell Physiol. 2009; 50: 2146-61.

[207] Jiang W, Fu X, Pan Q et al. Overexpression of AaWRKY1 leads to an enhanced content of artemisinin in Artemisia annua. Biomed Res Int. 2016; 2016: 7314971.

[208] Lv Z, Wang S, Zhang F et al. Overexpression of a novel NAC domain-containing transcription factor gene (AaNAC1) enhances the content of artemisinin and increases tolerance to drought and botrytis cinerea in Artemisia annua. Plant Cell Physiol. 2016; 57: 1961-71.

[209] Ji Y, Xiao J, Shen Y et al. Cloning and characterization of AabHLH1, a bHLH transcription factor that positively regulates artemisinin biosynthesis in Artemisia annua. Plant Cell Physiol. 2014; 55: 1592-604.

[210] Chu Y, Xiao S, Su H et al. Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng. Acta Pharm Sin B. 2018; 8: 666-77.

[211] Tamura K, Yoshida K, Hiraoka Y et al. The basic helix-loop-helix transcription factor GubHLH3 positively regulates soyasaponin biosynthetic genes in Glycyrrhiza uralensis. Plant Cell Physiol. 2018; 59: 778-91.

[212] Yin J, Li X, Zhan Y et al. Cloning and expression of BpMYC4 and BpbHLH9 genes and the role of BpbHLH9 in triterpenoid synthesis in birch. BMC Plant Biol. 2017; 17: 214.

[213] Mertens J, Pollier J, vanden Bossche R et al. The bHLH transcription factors TSAR1 and TSAR2 regulate triterpene saponin biosynthesis in Medicago truncatula. Plant Physiol. 2016; 170: 194-210.

[214] Tang Y, Li L, Yan T et al. AaEIN3 mediates the downregulation of artemisinin biosynthesis by ethylene signaling through promoting leaf senescence in Artemisia annua. Front Plant Sci. 2018; 9: 413.

[215] Matías-Hernández L, Jiang W, Yang K et al. AaMYB1 and its orthologue AtMYB61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana. Plant J. 2017; 90: 520-34.

[216] Liu T, Luo T, Guo X et al. PgMYB2, a MeJA-responsive transcription factor, positively regulates the dammarenediol synthase gene expression in Panax ginseng. Int J Mol Sci. 2019; 20: 2219.

[217] Reddy VA, Wang Q, Dhar N et al. Spearmint R2R3-MYB transcription factor MsMYB negatively regulates monoterpene production and suppresses the expression of geranyl diphosphate synthase large subunit (MsGPPS.LSU). Plant Biotechnol J. 2017; 15: 1105-19.

[218] Ding K, Pei T, Bai Z et al. SmMYB36, a novel R2R3-MYB transcription factor, enhances tanshinone accumulation and decreases phenolic acid content in salvia miltiorrhiza hairy roots. Sci Rep. 2017; 7: 5104.

[219] Zhang J, Zhou L, Zheng X et al. Overexpression of SmMYB9b enhances tanshinone concentration in salvia miltiorrhiza hairy roots. Plant Cell Rep. 2017; 36: 1297-309.

[220] Zhou ML, Hou HL, Zhu XM et al. Soybean transcription factor GmMYBZ2 represses catharanthine biosynthesis in hairy roots of Catharanthus roseus. Appl Microbiol Biot. 2011; 91: 1095-105.

[221] Chen X, Li J, Liu Y et al. PatSWC4, a methyl jasmonate-responsive MYB (v-myb avian myeloblastosis viral oncogene homolog)-related transcription factor, positively regulates patchoulol biosynthesis in Pogostemon cablin. Ind Crop Prod. 2020; 154: 112672.

[222] Li J, Chen X, Zhou X et al. Identification of trihelix transcription factors in Pogostemon cablin reveals PatGT-1 negatively regulates patchoulol biosynthesis. Ind Crop Prod. 2021; 161: 113182.

[223] Shi M, Zhou W, Zhang J et al. Methyl jasmonate induction of tanshinone biosynthesis in salvia miltiorrhiza hairy roots is mediated by jasmonate zim-domain repressor proteins. Sci Rep. 2016; 6: 20919.

[224] Zhou Y, Zhou X, Li Q et al. Molecular cloning, bioinformatics analysis, and transcriptional profiling of JAZ1 and JAZ2 from salvia miltiorrhiza. Biotechnol Appl Bioc. 2017; 64: 27-34.

[225] Wang Q, Reddy VA, Panicker D et al. Metabolic engineering of terpene biosynthesis in plants using a trichome-specific transcription factor MsYABBY5 from spearmint (Mentha spicata). Plant Biotechnol J. 2016; 14: 1619-32.

[226] Yamada Y, Nishida S, Shitan N et al. Genome-wide identification of AP2/ERF transcription factor-encoding genes in California poppy (Eschscholzia californica) and their expression profiles in response to methyl jasmonate. Sci Rep. 2020; 10: 18066.

[227] Wang CT, Liu H, Gao XS et al. Overexpression of G10H and ORCA3 in the hairy roots of Catharanthus roseus improves catharanthine production. Plant Cell Rep. 2010; 29: 887-94.

[228] van der Fits L, Memelink J . ORCA3, a jasmonate-responsive transcriptional regulator of plant primary and secondary metabolism. Science. 2000; 289: 295-7.

[229] Menke FL, Champion A, Kijne JW et al. A novel jasmonate- and elicitor-responsive element in the periwinkle secondary metabolite biosynthetic gene Str interacts with a jasmonate- and elicitor-inducible AP2-domain transcription factor, ORCA2. EMBO J. 1999; 18: 4455-63.

[230] Pan Q, Wang Q, Yuan F et al. Overexpression of ORCA3 and G10H in Catharanthus roseus plants regulated alkaloid biosynthesis and metabolism revealed by NMR-metabolomics. PLoS One. 2012; 7: e43038.

[231] Liu J, Gao F, Ren J et al. A novel AP2/ERF transcription factor CR1 regulates the accumulation of vindoline and serpentine in Catharanthus roseus. Front Plant Sci. 2017; 8: 2082.

[232] Deng X, Zhao L, Fang T et al. Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus. Hortic Res. 2018; 5: 29.

[233] Yamada Y, Kokabu Y, Chaki K et al. Isoquinoline alkaloid biosynthesis is regulated by a unique bHLH-type transcription factor in Coptis japonica. Plant Cell Physiol. 2011; 52: 1131-41.

[234] Chatel G, Montiel G, Pré M et al. CrMYC1, a Catharanthus roseus elicitor- and jasmonate-responsive bHLH transcription factor that binds the G-box element of the strictosidine synthase gene promoter. J Exp Bot. 2003; 54: 2587-8.

[235] Zhang H, Hedhili S, Montiel G et al. The basic helix-loop-helix transcription factor CrMYC2 controls the jasmonate-responsive expression of the ORCA genes that regulate alkaloid biosynthesis in Catharanthus roseus. Plant J. 2011; 67: 61-71.

[236] Singh SK et al. bHLH iridoid synthesis 3 is a member of a bHLH gene cluster regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Direct. 2021; 5: e00305.

[237] Pauw B, Hilliou FAO, Martin VS et al. Zinc finger proteins act as transcriptional repressors of alkaloid biosynthesis genes in Catharanthus roseus. J Biol Chem. 2004; 279: 52940-8.

[238] Kato N, Dubouzet E, Kokabu Y et al. Identification of a WRKY protein as a transcriptional regulator of benzylisoquinoline alkaloid biosynthesis in Coptis japonica. Plant Cell Physiol. 2007; 48: 8-18.

[239] Suttipanta N, Pattanaik S, Kulshrestha M et al. The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiol. 2011; 157: 2081-93.

[240] Sibéril Y, Benhamron S, Memelink J et al. Catharanthus roseus G-box binding factors 1 and 2 act as repressors of strictosidine synthase gene expression in cell cultures. Plant Mol Biol. 2001; 45: 477-88.

[241] Liu Y, Patra B, Pattanaik S et al. GATA and PIF transcription factors regulate light-induced biosynthesis of vindoline in Catharanthus. Plant Physiol. 2019; 180: 1316-50.

[242] Li CY et al. CrBPF1 overexpression alters transcript levels of terpenoid indole alkaloid biosynthetic and regulatory genes. Front Plant Sci. 2015; 6: 818.

[243] Rice ES, Green RE . New approaches for genome assembly and scaffolding. Annu Rev Anim Biosci. 2019; 7: 17-40.

[244] Wang J, Li J, Li Z et al. Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions. Hortic Res. 2022; 9: uhac021.

[245] Miga KH, Koren S, Rhie A et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020; 585: 79-84.

[246] Wang B, Yang X, Jia Y et al. High-quality Arabidopsis thaliana genome assembly with Nanopore and HiFi long reads. Genom Proteom Bioinf. 2022; 20: 4-13.

[247] Naish M, Alonge M, Wlodzimierz P et al. The genetic and epigenetic landscape of theArabidopsiscentromeres. Science. 2021; 374: eabi7489.

[248] Song JM, Xie WZ, Wang S et al. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol Plant. 2021; 14: 1757-67.

[249] Deng Y, Liu S, Zhangi Y et al. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol Plant. 2022; 15: 1268-84.

[250] Zhou Z, Tan H, Li Q et al. Trichome and ARTEMISININ regulator 2positively regulates trichome development and artemisinin biosynthesis inArtemisia annua. New Phytol. 2020; 228: 932-45.

[251] Chalvin C, Drevensek S, Dron M et al. Genetic control of glandular trichome development. Trends Plant Sci. 2020; 25: 477-87.

[252] Li Y, Kong D, Bai M et al. Correlation of the temporal and spatial expression patterns of HQT with the biosynthesis and accumulation of chlorogenic acid in Lonicera japonica flowers. Hortic Res. 2019; 6: 73.

[253] Cheng H, Concepcion GT, Feng X et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18: 170-5.

[254] Nützmann HW, Doerr D, Ramírez-Colmenero A et al. Active and repressed biosynthetic gene clusters have spatially distinct chromosome states. Proc Natl Acad Sci U S A. 2020; 117: 13800-9.

[255] Susniak K, Krysa M, Gieroba B et al. Recent developments of MALDI MSI application in plant tissues analysis. Acta Biochim Pol. 2020; 67: 277-81.

[256] Sun C, Ma S, Li L et al. Visualizing the distributions and spatiotemporal changes of metabolites in Panax notoginseng by MALDI mass spectrometry imaging. J Ginseng Res. 2021; 45: 726-33.

[257] Huang AC, Jiang T, Liu YX et al. A specialized metabolic network selectively modulates Arabidopsisroot microbiota. Science. 2019; 364: eaau6389.