{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T05:02:38Z","timestamp":1789448558511,"version":"build-2803163510"},"reference-count":100,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Beijing Life Science Academy","award":["2025100CD0050"],"award-info":[{"award-number":["2025100CD0050"]}]},{"DOI":"10.13039\/501100012421","name":"Agricultural Science and Technology Innovation Program","doi-asserted-by":"crossref","award":["CAAS-ZDRW202601"],"award-info":[{"award-number":["CAAS-ZDRW202601"]}],"id":[{"id":"10.13039\/501100012421","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Medicinal plants are major sources of therapeutic natural products, yet the cell-type-specific organization that governs metabolite biosynthesis, transport, and storage remains imperfectly resolved by organ-level omics. This review synthesizes studies published up to June 2026 that used single-cell, single-nucleus, spatial, metabolomic, and epigenomic approaches to medicinal plant systems, following a PRISMA-guided literature search across PubMed, Web of Science, Scopus, and CNKI. Emerging evidence shows that specialized metabolism is organized through discrete and often rare cell populations, including idioblasts, laticifers, glandular trichomes, secretory epidermal cells, internal phloem-associated parenchyma, cork and periderm cells, mesophyll cells, and other biosynthetic niches. Single-cell RNA sequencing has defined these populations and reconstructed developmental trajectories, whereas single-cell metabolomics and mass spectrometry imaging reveal that metabolite accumulation frequently diverges from biosynthetic gene expression because of intercellular transport, storage capacity, and subcellular compartmentation. Single-cell ATAC-seq and multiome profiling further identify cell-type-specific regulatory regions, transcription factors, and candidate promoters controlling metabolic competence. Together, these technologies are reshaping medicinal plant biology from pathway-centric catalogs into spatially and developmentally resolved cellular maps. We highlight how artificial intelligence (AI)-assisted integration can accelerate cell annotation, regulatory network inference, metabolite assignment, and prioritization of biosynthetic genes, transporters, and engineering targets. Future progress will depend on comparative medicinal plant atlases, improved recovery of recalcitrant tissues, matched transcriptomic, metabolomic, and spatial designs, and functional validation of cell-type-specific mechanisms.<\/jats:p>","DOI":"10.3390\/plants15182799","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T09:34:01Z","timestamp":1789378441000},"page":"2799","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-Cell Insights into Medicinal Plant Development and Metabolism"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1035-5078","authenticated-orcid":false,"given":"Baoping","family":"Jiang","sequence":"first","affiliation":[{"name":"Beijing Life Science Academy, Beijing 102200, China"},{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4148-0122","authenticated-orcid":false,"given":"Liang","family":"Le","sequence":"additional","affiliation":[{"name":"Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/s41573-020-00114-z","article-title":"Natural products in drug discovery: Advances and opportunities","volume":"20","author":"Atanasov","year":"2021","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"uhac223","DOI":"10.1093\/hr\/uhac223","article-title":"Natural products of medicinal plants: Biosynthesis and bioengineering in post-genomic era","volume":"9","author":"Guo","year":"2022","journal-title":"Hortic. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1038\/s41589-021-00822-6","article-title":"Adaptive mechanisms of plant specialized metabolism connecting chemistry to function","volume":"17","author":"Weng","year":"2021","journal-title":"Nat. Chem. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"17109","DOI":"10.1038\/nplants.2017.109","article-title":"Demystifying traditional herbal medicine with modern approach","volume":"3","author":"Li","year":"2017","journal-title":"Nat. Plants"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1126\/science.aat4096","article-title":"The opium poppy genome and morphinan production","volume":"362","author":"Guo","year":"2018","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1111\/tpj.13485","article-title":"Integrated omics analysis of specialized metabolism in medicinal plants","volume":"90","author":"Rai","year":"2017","journal-title":"Plant J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1111\/tpj.12608","article-title":"Natural products in Glycyrrhiza glabra (licorice) rhizome imaged at the cellular level by atmospheric pressure matrix-assisted laser desorption\/ionization tandem mass spectrometry imaging","volume":"80","author":"Li","year":"2014","journal-title":"Plant J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1142\/S0192415X10008007","article-title":"Mass spectrometric imaging of ginsenosides localization in Panax ginseng root","volume":"38","author":"Taira","year":"2010","journal-title":"Am. J. Chin. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1039\/b512615k","article-title":"Chemistry and biology of monoterpene indole alkaloid biosynthesis","volume":"23","author":"Maresh","year":"2006","journal-title":"Nat. Prod. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1126\/science.1217410","article-title":"Mining the biodiversity of plants: A revolution in the making","volume":"336","author":"Salim","year":"2012","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s11101-005-3748-2","article-title":"Taxol biosynthesis and molecular genetics","volume":"5","author":"Croteau","year":"2006","journal-title":"Phytochem. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1111\/pbi.12022","article-title":"Metabolic engineering of plant monoterpenes, sesquiterpenes and diterpenes--current status and future opportunities","volume":"11","author":"Lange","year":"2013","journal-title":"Plant Biotechnol. J."},{"key":"ref_13","first-page":"63","article-title":"Biosynthesis and biological functions of terpenoids in plants","volume":"148","author":"Tholl","year":"2015","journal-title":"Adv. Biochem. Eng. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1146\/annurev.arplant.043008.092035","article-title":"Metabolomics for functional genomics, systems biology, and biotechnology","volume":"61","author":"Saito","year":"2010","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1146\/annurev-genet-120116-024640","article-title":"The Genetics of Plant Metabolism","volume":"51","author":"Fernie","year":"2017","journal-title":"Annu. Rev. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/j.tplants.2017.01.003","article-title":"Leveraging Natural Variance towards Enhanced Understanding of Phytochemical Sunscreens","volume":"22","author":"Tohge","year":"2017","journal-title":"Trends Plant Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1104\/pp.16.01942","article-title":"Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants","volume":"173","author":"Zhang","year":"2017","journal-title":"Plant Physiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1146\/annurev-genet-120417-031237","article-title":"Metabolic Gene Clusters in Eukaryotes","volume":"52","author":"Scazzocchio","year":"2018","journal-title":"Annu. Rev. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1111\/nph.13981","article-title":"Plant metabolic clusters-from genetics to genomics","volume":"211","author":"Huang","year":"2016","journal-title":"New. Phytol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"107450","DOI":"10.1016\/j.biotechadv.2019.107450","article-title":"Application of next-generation sequencing for the identification of herbal products","volume":"37","author":"Lo","year":"2019","journal-title":"Biotechnol. Adv."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.trecan.2020.02.004","article-title":"Towards the Microbial Production of Plant-Derived Anticancer Drugs","volume":"6","author":"Courdavault","year":"2020","journal-title":"Trends Cancer"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1016\/j.tplants.2023.08.005","article-title":"Medicinal plants enter the single-cell multi-omics era","volume":"28","author":"Burlat","year":"2023","journal-title":"Trends Plant Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.tplants.2024.02.008","article-title":"Spatial multi-omics in medicinal plants: From biosynthesis pathways to industrial applications","volume":"29","author":"Chen","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2929","DOI":"10.1016\/j.apsb.2025.12.023","article-title":"Exploring specialized metabolic pathways in medicinal plants with single-cell and spatial omics","volume":"16","author":"Li","year":"2026","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1073\/pnas.1521959113","article-title":"Cell-specific localization of alkaloids in Catharanthus roseus stem tissue measured with Imaging MS and Single-cell MS","volume":"113","author":"Yamamoto","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1007\/s11101-015-9440-2","article-title":"Mass spectrometry imaging for plant biology: A review","volume":"15","author":"Boughton","year":"2016","journal-title":"Phytochem. Rev."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1039\/C3NP70100J","article-title":"Mass spectrometry imaging of plant metabolites--principles and possibilities","volume":"31","author":"Bjarnholt","year":"2014","journal-title":"Nat. Prod. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1016\/j.tplants.2016.04.007","article-title":"More than Pictures: When MS Imaging Meets Histology","volume":"21","author":"Dong","year":"2016","journal-title":"Trends Plant Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1105\/tpc.11.5.887","article-title":"Multicellular compartmentation of catharanthus roseus alkaloid biosynthesis predicts intercellular translocation of a pathway intermediate","volume":"11","year":"1999","journal-title":"Plant Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1365-313X.2004.02030.x","article-title":"Co-expression of three MEP pathway genes and geraniol 10-hydroxylase in internal phloem parenchyma of Catharanthus roseus implicates multicellular translocation of intermediates during the biosynthesis of monoterpene indole alkaloids and isoprenoid-derived primary metabolites","volume":"38","author":"Burlat","year":"2004","journal-title":"Plant J."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1007\/s00425-005-0167-y","article-title":"Epidermis is a pivotal site of at least four secondary metabolic pathways in Catharanthus roseus aerial organs","volume":"223","author":"Mahroug","year":"2006","journal-title":"Planta"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3606","DOI":"10.1038\/ncomms4606","article-title":"The seco-iridoid pathway from Catharanthus roseus","volume":"5","author":"Miettinen","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1093\/pcp\/pcx097","article-title":"Identification of Iridoid Glucoside Transporters in Catharanthus roseus","volume":"58","author":"Larsen","year":"2017","journal-title":"Plant Cell Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1016\/j.phytochem.2009.07.009","article-title":"Localization of enzymes of artemisinin biosynthesis to the apical cells of glandular secretory trichomes of Artemisia annua L.","volume":"70","author":"Olsson","year":"2009","journal-title":"Phytochemistry"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Olofsson, L., Engstr\u00f6m, A., Lundgren, A., and Brodelius, P.E. (2011). Relative expression of genes of terpene metabolism in different tissues of Artemisia annua L.. BMC Plant Biol., 11.","DOI":"10.1186\/1471-2229-11-45"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/S0031-9422(99)00308-8","article-title":"Differential accumulation of isoprenoids in glanded and glandless Artemisia annua L.","volume":"52","author":"Tellez","year":"1999","journal-title":"Phytochemistry"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1105\/tpc.015396","article-title":"A tale of three cell types: Alkaloid biosynthesis is localized to sieve elements in opium poppy","volume":"15","author":"Bird","year":"2003","journal-title":"Plant Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"13957","DOI":"10.1073\/pnas.0405704101","article-title":"The roles of latex and the vascular bundle in morphine biosynthesis in the opium poppy, Papaver somniferum","volume":"101","author":"Weid","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/s41467-024-55485-3","article-title":"Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots","volume":"16","author":"Wang","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"157204","DOI":"10.1016\/j.phymed.2025.157204","article-title":"Single-cell omics reveal the mechanisms of traditional Chinese medicines","volume":"147","author":"Jiang","year":"2025","journal-title":"Phytomedicine"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s13059-016-0931-2","article-title":"The potential of single-cell profiling in plants","volume":"17","author":"Efroni","year":"2016","journal-title":"Genome Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/j.molp.2021.01.001","article-title":"Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level","volume":"14","author":"Farmer","year":"2021","journal-title":"Mol. Plant"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1111\/nph.16138","article-title":"The complexity of intercellular localisation of alkaloids revealed by single-cell metabolomics","volume":"224","author":"Yamamoto","year":"2019","journal-title":"New Phytol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41477-022-01291-y","article-title":"Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism","volume":"9","author":"Sun","year":"2023","journal-title":"Nat. Plants"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"23891","DOI":"10.1021\/jacs.4c06336","article-title":"Quantitative Single-Cell Mass Spectrometry Provides a Highly Resolved Analysis of Natural Product Biosynthesis Partitioning in Plants","volume":"146","author":"Vu","year":"2024","journal-title":"J. Am. Chem. Soc."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e2411276","DOI":"10.1002\/advs.202411276","article-title":"Single-Cell Simultaneous Metabolome and Transcriptome Profiling Revealing Metabolite-Gene Correlation Network","volume":"12","author":"Mao","year":"2025","journal-title":"Adv. Sci."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/s41589-023-01327-0","article-title":"Single-cell multi-omics in the medicinal plant Catharanthus roseus","volume":"19","author":"Li","year":"2023","journal-title":"Nat. Chem. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/nph.20208","article-title":"Cell-type-aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus","volume":"245","author":"Li","year":"2025","journal-title":"New Phytol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3041","DOI":"10.1016\/j.cell.2021.04.014","article-title":"A cis-regulatory atlas in maize at single-cell resolution","volume":"184","author":"Marand","year":"2021","journal-title":"Cell"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2889","DOI":"10.1111\/jipb.70272","article-title":"Single-cell insights into plant growth, adaptation, and evolution","volume":"68","author":"Wang","year":"2026","journal-title":"J. Integr. Plant Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nmeth.4071","article-title":"Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-\u03bcm lateral resolution","volume":"14","author":"Kompauer","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1039\/C9NP00038K","article-title":"Imaging mass spectrometry for natural products discovery: A review of ionization methods","volume":"37","author":"Spraker","year":"2020","journal-title":"Nat. Prod. Rep."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Dong, Y., Li, B., Malitsky, S., Rogachev, I., Aharoni, A., Kaftan, F., Svato\u0161, A., and Franceschi, P. (2016). Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review. Front. Plant Sci., 7.","DOI":"10.3389\/fpls.2016.00060"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/s41586-025-09090-z","article-title":"Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III","volume":"643","author":"McClune","year":"2025","journal-title":"Nature"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s002530100757","article-title":"Taxol: Biosynthesis, molecular genetics, and biotechnological applications","volume":"57","author":"Jennewein","year":"2001","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1126\/science.1191652","article-title":"Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli","volume":"330","author":"Ajikumar","year":"2010","journal-title":"Science"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1016\/j.molp.2024.08.003","article-title":"Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John\u2019s wort","volume":"17","author":"Wu","year":"2024","journal-title":"Mol. Plant"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"4461","DOI":"10.1111\/pbi.70198","article-title":"Single-cell sequencing and mass spectrometry imaging reveal the multicellular compartmentalization map of plant triterpenes: A ginsenoside in Panax ginseng example","volume":"23","author":"Wang","year":"2025","journal-title":"Plant Biotechnol. J."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"uhaf202","DOI":"10.1093\/hr\/uhaf202","article-title":"Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis in Panax root tips","volume":"12","author":"Yang","year":"2025","journal-title":"Hortic. Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"8646","DOI":"10.1038\/s41467-025-63770-y","article-title":"Single-nucleus transcriptomics reveal the morphogenesis and artemisinin biosynthesis in Artemisia annua glandular trichomes","volume":"16","author":"Zhang","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Zhou, P., Chen, H., Dang, J., Shi, Z., Shao, Y., Liu, C., Fan, L., and Wu, Q. (2022). Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.988594"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1111\/nph.71285","article-title":"Cross-stage single-cell and spatial metabolome analyses reveal periderm specialization and tanshinone biosynthesis in Salvia miltiorrhiza roots","volume":"251","author":"Liu","year":"2026","journal-title":"New Phytol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1111\/pbi.70687","article-title":"Cell-Specific Expression and Cellular Compartmental Regulation in Camptothecin Biosynthesis","volume":"24","author":"Hao","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e14508","DOI":"10.1111\/ppl.14508","article-title":"ScRNA-seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves","volume":"176","author":"Wang","year":"2024","journal-title":"Physiol. Plant."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2226","DOI":"10.1111\/pbi.70464","article-title":"Genome and Single-Cell Transcriptome Reveal the Evolution of Holoparasitic Plants: A Case Study of Cistanche deserticola","volume":"24","author":"Zhang","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1111\/pbi.70534","article-title":"Mass Spectrometry Imaging Combined With Single-Cell Transcriptional Profiling Reveals the Multidimensional Spatial Distributions and Biosynthetic Pathways of Medicinal Components in Andrographis paniculata","volume":"24","author":"Zeng","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Li, R., Du, K., Zhang, C., Shen, X., Yun, L., Wang, S., Li, Z., Sun, Z., Wei, J., and Li, Y. (2024). Single-cell transcriptome profiling reveals the spatiotemporal distribution of triterpenoid saponin biosynthesis and transposable element activity in Gynostemma pentaphyllum shoot apexes and leaves. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1394587"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/s42003-025-09434-5","article-title":"Construction of a single-cell transcriptome atlas for Pogostemon cablin embryoids reveals PcNAC048 as a dual regulator coordinating lateral root morphogenesis and patchouli alcohol biosynthesis","volume":"9","author":"Wang","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"2997","DOI":"10.1111\/pbi.70094","article-title":"Resolving floral development dynamics using genome and single-cell temporal transcriptome of Dendrobium devonianum","volume":"23","author":"Wang","year":"2025","journal-title":"Plant Biotechnol. J."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"n71","DOI":"10.1136\/bmj.n71","article-title":"The PRISMA 2020 statement: An updated guideline for reporting systematic reviews","volume":"372","author":"Page","year":"2021","journal-title":"BMJ"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1104\/pp.18.01482","article-title":"Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells","volume":"179","author":"Ryu","year":"2019","journal-title":"Plant Physiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1105\/tpc.18.00785","article-title":"Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana","volume":"31","author":"Alexandre","year":"2019","journal-title":"Plant Cell"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"16208","DOI":"10.1038\/nplants.2016.208","article-title":"An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole","volume":"3","author":"Payne","year":"2017","journal-title":"Nat. Plants"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1111\/pbi.70362","article-title":"Metabolomic and Single-Cell Transcriptomic Analyses Shed Light on Secondary Metabolite Profiling and Potential Developmental Dynamics of Glandular Trichomes in Artemisia argyi","volume":"24","author":"Dong","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"4455","DOI":"10.1093\/emboj\/18.16.4455","article-title":"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","volume":"18","author":"Menke","year":"1999","journal-title":"Embo J."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1104\/pp.102.018127","article-title":"Laser capture microdissection of cells from plant tissues","volume":"132","author":"Kerk","year":"2003","journal-title":"Plant Physiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41586-023-06053-0","article-title":"A pan-grass transcriptome reveals patterns of cellular divergence in crops","volume":"617","author":"Guillotin","year":"2023","journal-title":"Nature"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1111\/tpj.15772","article-title":"Advances and applications of single-cell omics technologies in plant research","volume":"110","author":"Mo","year":"2022","journal-title":"Plant J."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1016\/j.molp.2023.10.008","article-title":"Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells","volume":"16","author":"Lin","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1105\/tpc.17.00581","article-title":"Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules","volume":"30","author":"Maher","year":"2018","journal-title":"Plant Cell"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1038\/s41477-019-0548-z","article-title":"The prevalence, evolution and chromatin signatures of plant regulatory elements","volume":"5","author":"Lu","year":"2019","journal-title":"Nat. Plants"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2308384","DOI":"10.1002\/advs.202308384","article-title":"Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level","volume":"11","author":"Liu","year":"2024","journal-title":"Adv. Sci."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1111\/tpj.13422","article-title":"High spatial resolution mass spectrometry imaging reveals the genetically programmed, developmental modification of the distribution of thylakoid membrane lipids among individual cells of maize leaf","volume":"89","author":"Klein","year":"2017","journal-title":"Plant J."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"6196","DOI":"10.1073\/pnas.0711730105","article-title":"Nonuniform distribution of glucosinolates in Arabidopsis thaliana leaves has important consequences for plant defense","volume":"105","author":"Shroff","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"100630","DOI":"10.1016\/j.xplc.2023.100630","article-title":"Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves","volume":"4","author":"Zhan","year":"2023","journal-title":"Plant Commun."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1111\/tpj.16315","article-title":"Integrated mass spectrometry imaging and single-cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems","volume":"115","author":"Yu","year":"2023","journal-title":"Plant J."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1111\/pbi.70386","article-title":"Single Cell Multi-Omics Reveals Rare Biosynthetic Cell Types in the Medicinal Tree Camptotheca acuminata","volume":"24","author":"Bui","year":"2026","journal-title":"Plant Biotechnol. J."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1016\/j.molp.2018.03.015","article-title":"The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis","volume":"11","author":"Shen","year":"2018","journal-title":"Mol. Plant"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"100467","DOI":"10.1016\/j.cpb.2025.100467","article-title":"Single-cell RNA sequencing reveals transcriptional regulation and metabolic pathways of terpenoid biosynthesis in developing Cinnamomum camphora leaf cells","volume":"42","author":"Qin","year":"2025","journal-title":"Curr. Plant Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"2094","DOI":"10.1093\/plphys\/kiae199","article-title":"Global dynamics and cytokinin participation of salt gland development trajectory in recretohalophyte Limonium bicolor","volume":"195","author":"Zhao","year":"2024","journal-title":"Plant Physiol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"15830","DOI":"10.1073\/pnas.1307504110","article-title":"ATP-binding cassette transporter controls leaf surface secretion of anticancer drug components in Catharanthus roseus","volume":"110","author":"Yu","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41587-021-01206-w","article-title":"A Python library for probabilistic analysis of single-cell omics data","volume":"40","author":"Gayoso","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/s41587-021-01139-4","article-title":"Cell2location maps fine-grained cell types in spatial transcriptomics","volume":"40","author":"Kleshchevnikov","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1038\/s41592-021-01264-7","article-title":"Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram","volume":"18","author":"Biancalani","year":"2021","journal-title":"Nat. Methods"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"e57613","DOI":"10.7554\/eLife.57613","article-title":"Accurate and versatile 3D segmentation of plant tissues at cellular resolution","volume":"9","author":"Wolny","year":"2020","journal-title":"Elife"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/s41592-019-0344-8","article-title":"SIRIUS 4: A rapid tool for turning tandem mass spectra into metabolite structure information","volume":"16","author":"Fleischauer","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Huber, F., Ridder, L., Verhoeven, S., Spaaks, J.H., Diblen, F., Rogers, S., and van der Hooft, J.J.J. (2021). Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. PLoS Comput. Biol., 17.","DOI":"10.1371\/journal.pcbi.1008724"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2799\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T04:20:43Z","timestamp":1789446043000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2799"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":100,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182799"],"URL":"https:\/\/doi.org\/10.3390\/plants15182799","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]}}}