{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T05:06:29Z","timestamp":1789103189658,"version":"build-2803163510"},"reference-count":287,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Plant specialized metabolism changes throughout development, but developmental context remains inconsistently incorporated into phytochemical interpretation. This integrative narrative review synthesizes evidence on chemical ontogeny in plants, defined here as the qualitative and quantitative reorganization of specialized metabolism along plant and organ development. We distinguish ontogenetic variation from phenology, seasonality, organ maturation, developmental plasticity, and environmentally induced chemical plasticity, and examine the genetic, hormonal, anatomical, ecological, and analytical processes that generate stage-dependent chemical profiles. Across seeds, seedlings, vegetative organs, reproductive structures, fruits, and senescent tissues, the evidence shows recurrent changes in metabolite abundance, composition, spatial allocation, and bioactivity. These trajectories can alter ecological interactions, marker stability, harvest recommendations, and the reproducibility of botanical raw materials. Analytical strategies should therefore be selected according to the biological question and available resources, ranging from validated targeted or single-omics designs to spatial, single-cell, and multi-omics integration when mechanistically justified. Chemical ontogeny is proposed not as evidence that developmental metabolism is newly discovered, but as an operational framework for stage-aware sampling, reporting, interpretation, quality control, and bioprospecting.<\/jats:p>","DOI":"10.3390\/plants15182756","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T08:05:43Z","timestamp":1788941143000},"page":"2756","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chemical Ontogeny in Plants: Developmental Dynamics of Specialized Metabolism and Implications for Ecology, Quality Control, and Bioprospecting"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-5319-5457","authenticated-orcid":false,"given":"Dannily Augusto","family":"Rebou\u00e7as","sequence":"first","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorraynne","family":"Oliveira-Souza","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"},{"name":"Research Institute of the Rio de Janeiro Botanical Garden, Rua Pacheco Le\u00e3o 915, Jardim Bot\u00e2nico, Rio de Janeiro 22460-030, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamara do Nascimento da","family":"Silva","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4220-0935","authenticated-orcid":false,"given":"Rodrigo Guimar\u00e3es de","family":"Deus","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3119-9131","authenticated-orcid":false,"given":"Orlando Maia","family":"Barboza","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara Cabral","family":"Noronha","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe Barreto de","family":"Almeida","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4015-1184","authenticated-orcid":false,"given":"Gustavo Borges","family":"Andrade","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3060-0395","authenticated-orcid":false,"given":"Davyson de Lima","family":"Moreira","sequence":"additional","affiliation":[{"name":"Research Institute of the Rio de Janeiro Botanical Garden, Rua Pacheco Le\u00e3o 915, Jardim Bot\u00e2nico, Rio de Janeiro 22460-030, RJ, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4443-1008","authenticated-orcid":false,"given":"Ygor Jess\u00e9","family":"Ramos","sequence":"additional","affiliation":[{"name":"Farm\u00e1cia da Terra Laboratory, Faculty of Pharmacy, Federal University of Bahia, Rua Bar\u00e3o de Jeremoabo, 147, Ondina, Salvador 40170-115, BA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nrg3541","article-title":"Spatiotemporal signalling in plant development","volume":"14","author":"Sparks","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.tplants.2021.10.005","article-title":"Spatiotemporal limitations in plant biology research","volume":"27","year":"2022","journal-title":"Trends Plant Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"102530","DOI":"10.1016\/j.pbi.2024.102530","article-title":"Spatiotemporal regulation of plant cell division","volume":"79","author":"Bouchez","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/s43450-022-00327-w","article-title":"Chemophenetic and chemodiversity approaches: New insights on modern study of plant secondary metabolite diversity at different spatiotemporal and organizational scales","volume":"33","author":"Ramos","year":"2023","journal-title":"Rev. Bras. De Farmacogn."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1126\/science.129.3361.1466","article-title":"The raison d\u2019\u00eatre of secondary plant substances","volume":"129","author":"Fraenkel","year":"1959","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0031-9422(03)00300-5","article-title":"Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective","volume":"64","author":"Wink","year":"2003","journal-title":"Phytochemistry"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2831","DOI":"10.1016\/j.phytochem.2007.09.017","article-title":"From waste products to ecochemicals: Fifty years research of plant secondary metabolism","volume":"68","author":"Hartmann","year":"2007","journal-title":"Phytochemistry"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1146\/annurev-arplant-042110-103814","article-title":"Convergent evolution in plant specialized metabolism","volume":"62","author":"Pichersky","year":"2011","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1104\/pp.20.00433","article-title":"Plant secondary metabolites as defenses, regulators, and primary metabolites: The blurred functional trichotomy","volume":"184","author":"Erb","year":"2020","journal-title":"Plant Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1146\/annurev-arplant-060223-013842","article-title":"Using synthetic biology to understand the function of plant specialized metabolites","volume":"75","author":"Bai","year":"2024","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1016\/j.tplants.2025.02.010","article-title":"Evolution of plant specialized metabolites: Beyond ecological drivers","volume":"30","author":"Xu","year":"2025","journal-title":"Trends Plant Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1086\/282909","article-title":"Adaptive patterns in alkaloid physiology","volume":"108","author":"McKey","year":"1974","journal-title":"Am. Nat."},{"key":"ref_13","unstructured":"Rosenthal, G.A., and Janzen, D.H. (1979). Evolution of plant chemical defense against herbivores. Herbivores: Their Interaction with Secondary Plant Metabolites, Academic Press."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1111\/j.1600-0706.2009.17206.x","article-title":"Plant ontogeny and chemical defence: Older seedlings are better defended","volume":"118","author":"Elger","year":"2009","journal-title":"Oikos"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1086\/650722","article-title":"The ontogeny of plant defense and herbivory: Characterizing general patterns using meta-analysis","volume":"175","author":"Barton","year":"2010","journal-title":"Am. Nat."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/ele.12744","article-title":"Future directions in the ontogeny of plant defence: Understanding the evolutionary causes and consequences","volume":"20","author":"Barton","year":"2017","journal-title":"Ecol. Lett."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Wang, Z., Xie, C., Wu, Y., Liu, H., Zhang, X., Du, H., Li, X., and Zhang, C. (2024). Integrated metabolomics and transcriptomics analyses reveal the regulatory mechanisms of anthocyanin and carotenoid accumulation in the peel of Coffea arabica. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251910754"},{"key":"ref_18","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_19","doi-asserted-by":"crossref","unstructured":"Gaia, A.M., Yamaguchi, L.F., Guerrero-Perilla, C., and Kato, M.J. (2021). Ontogenetic changes in the chemical profiles of Piper species. Plants, 10.","DOI":"10.3390\/plants10061085"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13020-022-00601-y","article-title":"Plant metabolomics: A new strategy and tool for quality evaluation of Chinese medicinal materials","volume":"17","author":"Xiao","year":"2022","journal-title":"Chin. Med."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Ji, P., Yang, X., and Zhao, X. (2024). Application of metabolomics in quality control of traditional Chinese medicines: A review. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1463666"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Haeckel, E. (1866). Generelle Morphologie der Organismen, Georg Reimer.","DOI":"10.1515\/9783110848281"},{"key":"ref_23","unstructured":"Gould, S.J. (1977). Ontogeny and Phylogeny, Harvard University Press."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"R1279","DOI":"10.1016\/j.cub.2019.10.064","article-title":"Ernst Haeckel in the history of biology","volume":"29","author":"Levit","year":"2019","journal-title":"Curr. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Goethe, J.W. (1790). Versuch die Metamorphose der Pflanzen zu Erkl\u00e4ren, Ettinger.","DOI":"10.5962\/bhl.title.127448"},{"key":"ref_26","unstructured":"Hofmeister, W. (1868). Allgemeine Morphologie der Gew\u00e4chse, Wilhelm Engelmann."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Goebel, K. (1900). Organography of Plants, Especially of the Archegoniatae and Spermaphyta, Clarendon Press.","DOI":"10.5962\/bhl.title.44288"},{"key":"ref_28","unstructured":"Troll, W. (1943). Vergleichende Morphologie der H\u00f6heren Pflanzen, Gebr\u00fcder Borntraeger."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.2307\/3558347","article-title":"The science of plant morphology: Definition, history, and role in modern biology","volume":"88","author":"Kaplan","year":"2001","journal-title":"Am. J. Bot."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1006\/anbo.2001.1544","article-title":"Plant morphology: The historic concepts of Wilhelm Troll, Walter Zimmermann and Agnes Arber","volume":"88","year":"2001","journal-title":"Ann. Bot."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1126\/science.250.4983.923","article-title":"Phase change and the regulation of shoot morphogenesis in plants","volume":"250","author":"Poethig","year":"1990","journal-title":"Science"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"S105","DOI":"10.1086\/314215","article-title":"An essay on juvenility, phase change, and heteroblasty in seed plants","volume":"160","author":"Jones","year":"1999","journal-title":"Int. J. Plant Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1093\/aob\/mcl260","article-title":"Plant architecture: A dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny","volume":"99","author":"Caraglio","year":"2007","journal-title":"Ann. Bot."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s12229-010-9062-8","article-title":"Heteroblasty: A review","volume":"77","author":"Zotz","year":"2011","journal-title":"Bot. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1126\/science.52.1340.229","article-title":"Effects produced by X-Ray energy acting upon frogs\u2019 ova in early developmental stages","volume":"52","author":"Baldwin","year":"1920","journal-title":"Science"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1085\/jgp.9.4.405","article-title":"Physiological ontogeny. A. Chicken embryos. VII. The concentration of the organic constituents and the calorific value as functions of age","volume":"9","author":"Murray","year":"1926","journal-title":"J. Gen. Physiol."},{"key":"ref_37","first-page":"145","article-title":"Some comparisons of chemical ontogeny with chemical phylogeny in vascular plants","volume":"8","author":"McNair","year":"1945","journal-title":"Lloydia"},{"key":"ref_38","first-page":"203","article-title":"Gedanken \u00fcber die theoretische Bedeutung der chemisch-ontogenetischen und chemisch-systematischen Betrachtung von Arzneipflanzen","volume":"29","author":"Hegnauer","year":"1954","journal-title":"Pharm. Acta Helv."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1007\/s00442-007-0787-y","article-title":"Ontogenetic and temporal trajectories of chemical defence in a cyanogenic eucalypt","volume":"153","author":"Goodger","year":"2007","journal-title":"Oecologia"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1111\/1365-2435.14464","article-title":"The ontogenetic dimension of plant functional ecology","volume":"38","author":"Barton","year":"2024","journal-title":"Funct. Ecol."},{"key":"ref_41","unstructured":"Waddington, C.H. (1957). The Strategy of the Genes, George Allen & Unwin."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/B978-0-12-396968-2.00005-1","article-title":"Vegetative phase change and shoot maturation in plants","volume":"105","author":"Poethig","year":"2013","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_43","unstructured":"Gilbert, S.F. (2014). Developmental Biology, Sinauer Associates. [10th ed.]."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.devcel.2023.11.010","article-title":"Temporal regulation of vegetative phase change in plants","volume":"59","author":"Poethig","year":"2024","journal-title":"Dev. Cell"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1093\/jexbot\/51.352.1769","article-title":"Aspects of seasonality","volume":"51","author":"Battey","year":"2000","journal-title":"J. Exp. Bot."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1146\/annurev-ecolsys-102722-011653","article-title":"Effects of phenology on plant community assembly and structure","volume":"55","author":"Cleland","year":"2024","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1111\/nph.18617","article-title":"Phenological physiology: Seasonal patterns of plant stress tolerance in a changing climate","volume":"237","author":"Grossman","year":"2023","journal-title":"New Phytol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1111\/nph.12526","article-title":"Explaining intraspecific diversity in plant secondary metabolites in an ecological context","volume":"201","author":"Moore","year":"2014","journal-title":"New Phytol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"20230347","DOI":"10.1098\/rstb.2023.0347","article-title":"Evolution of plant metabolism: The state-of-the-art","volume":"379","author":"Fernie","year":"2024","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.tplants.2014.11.002","article-title":"Plasticity of specialized metabolism as mediated by dynamic metabolons","volume":"20","author":"Laursen","year":"2015","journal-title":"Trends Plant Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/j.tree.2005.05.001","article-title":"Facing herbivory as you grow up: The ontogeny of resistance in plants","volume":"20","author":"Boege","year":"2005","journal-title":"Trends Ecol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1104\/pp.110.161620","article-title":"The past, present, and future of vegetative phase change","volume":"154","author":"Poethig","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"4117","DOI":"10.1242\/dev.063511","article-title":"The control of developmental phase transitions in plants","volume":"138","author":"Huijser","year":"2011","journal-title":"Development"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"de Andrade Melo-Sterza, F., and Poehland, R. (2021). Lipid metabolism in bovine oocytes and early embryos under in vivo, in vitro, and stress condition. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22073421"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"e14365","DOI":"10.1111\/ele.14365","article-title":"The evolution of chemodiversity in plants-From verbal to quantitative models","volume":"27","author":"Thon","year":"2024","journal-title":"Ecol. Lett."},{"key":"ref_56","first-page":"265","article-title":"Einheitliche Codierung der ph\u00e4nologischen Entwicklungsstadien mono- und dikotyler Pflanzen: Erweiterte BBCH-Skala","volume":"44","author":"Hack","year":"1992","journal-title":"Nachrichtenblatt Des Dtsch. Pflanzenschutzdienstes"},{"key":"ref_57","unstructured":"Meier, U. (2001). Growth Stages of Mono- and Dicotyledonous Plants: BBCH Monograph, Federal Biological Research Centre for Agriculture and Forestry. [2nd ed.]."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1146\/annurev-arplant-050718-095859","article-title":"Leaf senescence: Systems and dynamics aspects","volume":"70","author":"Woo","year":"2019","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/tpj.16391","article-title":"How metabolism and development are intertwined in space and time","volume":"116","author":"Caldana","year":"2023","journal-title":"Plant J."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"de Brito-Machado, D., Ramos, Y.J., Defaveri, A.C.A.E., de Queiroz, G.A., Guimar\u00e3es, E.F., and de Lima Moreira, D. (2022). Volatile chemical variation of essential oils and their correlation with insects, phenology, ontogeny and microclimate: Piper mollicomum Kunth, a case of study. Plants, 11.","DOI":"10.3390\/plants11243535"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/s12033-017-0056-1","article-title":"Specialized plant metabolism characteristics and impact on target molecule biotechnological production","volume":"60","author":"Matsuura","year":"2018","journal-title":"Mol. Biotechnol."},{"key":"ref_62","first-page":"22","article-title":"Emerging mechanistic insights into the regulation of specialized metabolism in plants","volume":"9","author":"Papon","year":"2023","journal-title":"Nat. Plants"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s43897-023-00059-y","article-title":"Multilayered regulation of secondary metabolism in medicinal plants","volume":"3","author":"Zhao","year":"2023","journal-title":"Mol. Hortic."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1105\/tpc.111.084525","article-title":"Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor","volume":"23","author":"Gou","year":"2011","journal-title":"Plant Cell"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1111\/tpj.12712","article-title":"The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants","volume":"80","author":"Cui","year":"2014","journal-title":"Plant J."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/s41438-020-00341-w","article-title":"miR156 regulates anthocyanin biosynthesis through SPL targets and other microRNAs in poplar","volume":"7","author":"Wang","year":"2020","journal-title":"Hortic. Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"uhad293","DOI":"10.1093\/hr\/uhad293","article-title":"miR156b-targeted VvSBP8\/13 functions downstream of the abscisic acid signal to regulate anthocyanins biosynthesis in grapevine fruit under drought","volume":"11","author":"Guo","year":"2024","journal-title":"Hortic. Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1093\/pcp\/pcn077","article-title":"Jasmonate-induced nicotine formation in tobacco is mediated by tobacco COI1 and JAZ genes","volume":"49","author":"Shoji","year":"2008","journal-title":"Plant Cell Physiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"3390","DOI":"10.1105\/tpc.110.078543","article-title":"Clustered transcription factor genes regulate nicotine biosynthesis in tobacco","volume":"22","author":"Shoji","year":"2010","journal-title":"Plant Cell"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1093\/pcp\/pcr063","article-title":"Tobacco MYC2 regulates jasmonate-inducible nicotine biosynthesis genes directly and by way of the NIC2-locus ERF genes","volume":"52","author":"Shoji","year":"2011","journal-title":"Plant Cell Physiol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2638","DOI":"10.1093\/pcp\/pcz161","article-title":"Plant specialized metabolism regulated by jasmonate signaling","volume":"60","author":"Chen","year":"2019","journal-title":"Plant Cell Physiol."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Luo, L., Wang, Y., Qiu, L., Han, X., Zhu, Y., Liu, L., Man, M., Li, F., Ren, M., and Xing, Y. (2023). MYC2: A master switch for plant physiological processes and specialized metabolite synthesis. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24043511"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"2608","DOI":"10.1038\/s41467-023-38207-z","article-title":"Coordinated regulation of vegetative phase change by brassinosteroids and the age pathway in Arabidopsis","volume":"14","author":"Zhou","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1007\/s42994-021-00053-2","article-title":"Reprogramming plant specialized metabolism by manipulating protein kinases","volume":"2","author":"Lyu","year":"2021","journal-title":"aBIOTECH"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1111\/j.1365-313X.2008.03432.x","article-title":"Harnessing plant trichome biochemistry for the production of useful compounds","volume":"54","author":"Schilmiller","year":"2008","journal-title":"Plant J."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1104\/pp.17.00727","article-title":"Plant glandular trichomes: Natural cell factories of high biotechnological interest","volume":"175","author":"Huchelmann","year":"2017","journal-title":"Plant Physiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/s41438-021-00592-1","article-title":"Glandular trichomes: New focus on horticultural crops","volume":"8","author":"Feng","year":"2021","journal-title":"Hortic. Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.phytochem.2016.08.006","article-title":"Regulation of plant secondary metabolism and associated specialized cell development by MYBs and bHLHs","volume":"131","author":"Chezem","year":"2016","journal-title":"Phytochemistry"},{"key":"ref_79","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_80","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_81","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_82","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1111\/nph.70712","article-title":"A cell-type-specific regulon controlling monoterpene indole alkaloid biosynthesis with feedback and feedforward activation loops","volume":"249","author":"Li","year":"2026","journal-title":"New Phytol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"108258","DOI":"10.1016\/j.biotechadv.2023.108258","article-title":"Subcellular compartmentalization in the biosynthesis and engineering of plant natural products","volume":"69","author":"Yao","year":"2023","journal-title":"Biotechnol. Adv."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1111\/j.1742-4658.2010.07994.x","article-title":"The subcellular organization of strictosidine biosynthesis in Catharanthus roseus epidermis highlights several trans-tonoplast translocations of intermediate metabolites","volume":"278","author":"Guirimand","year":"2011","journal-title":"FEBS J."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"102616","DOI":"10.1016\/j.pbi.2024.102616","article-title":"The multicellular compartmentation of plant specialized metabolism","volume":"81","author":"Shen","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_86","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_87","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1105\/tpc.113.110890","article-title":"Integration of biosynthesis and long-distance transport establish organ-specific glucosinolate profiles in vegetative Arabidopsis","volume":"25","author":"Andersen","year":"2013","journal-title":"Plant Cell"},{"key":"ref_88","first-page":"1326","article-title":"The vacuolar transportome of plant specialized metabolites","volume":"59","author":"Martinoia","year":"2018","journal-title":"Plant Cell Physiol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Wu, M., Northen, T.R., and Ding, Y. (2023). Stressing the importance of plant specialized metabolites: Omics-based approaches for discovering specialized metabolism in plant stress responses. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1272363"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"102620","DOI":"10.1016\/j.pbi.2024.102620","article-title":"Unlocking specialized metabolism in medicinal plant biotechnology through plant-microbiome interactions","volume":"82","author":"Laffon","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"kiaf375","DOI":"10.1093\/plphys\/kiaf375","article-title":"Plant metabolism: Zoom in to the single-cell level","volume":"199","author":"Ntelkis","year":"2025","journal-title":"Plant Physiol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Felisberto, J.S., Machado, D.B., Assun\u00e7\u00e3o, J.A., Massau, S.A., Queiroz, G.A.D., Guimar\u00e3es, E.F., Ramos, Y.J., and Moreira, D.D.L. (2024). Spatio-Temporal Variations of Volatile Metabolites as an Eco-Physiological Response of a Native Species in the Tropical Forest. Plants, 13.","DOI":"10.3390\/plants13182599"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/j.molp.2017.02.006","article-title":"Insect resistance: An emerging molecular framework linking plant age and JA signaling","volume":"10","author":"Gaquerel","year":"2017","journal-title":"Mol. Plant"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/S0031-9422(02)00549-6","article-title":"Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana","volume":"62","author":"Brown","year":"2003","journal-title":"Phytochemistry"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1007\/s004250100659","article-title":"Composition and content of glucosinolates in developing Arabidopsis thaliana","volume":"214","author":"Petersen","year":"2002","journal-title":"Planta"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"e17231","DOI":"10.1111\/tpj.17231","article-title":"Multi-omic analyses unveil contrasting composition and spatial distribution of specialized metabolites in seeds of Camelina sativa and other Brassicaceae","volume":"121","author":"Barreda","year":"2025","journal-title":"Plant J."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"110471","DOI":"10.1016\/j.plantsci.2020.110471","article-title":"Specialized phenolic compounds in seeds: Structures, functions, and regulations","volume":"296","author":"Corso","year":"2020","journal-title":"Plant Sci."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S0031-9422(99)00498-7","article-title":"Variation of DIMBOA and related compounds content in relation to the age and plant organ in maize","volume":"53","author":"Cambier","year":"2000","journal-title":"Phytochemistry"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"154206","DOI":"10.1016\/j.jplph.2024.154206","article-title":"Metabolic control of seed germination in legumes","volume":"295","author":"Gasparini","year":"2024","journal-title":"J. Plant Physiol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s11101-012-9250-8","article-title":"Secondary metabolites during early development in plants","volume":"12","year":"2013","journal-title":"Phytochem. Rev."},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Ye, L., Bai, F., Zhang, L., Luo, M., Gao, L., Wang, Z., Peng, J., Chen, Q., and Luo, X. (2023). Transcriptome and metabolome analyses of anthocyanin biosynthesis in post-harvest fruits of a full red-type kiwifruit (Actinidia arguta) \u2018Jinhongguan\u2019. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1280970"},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Li, J., Geng, Z., Yuan, Y., Wang, M., Zhang, Y., and Wang, J. (2025). Investigation on rational utilization of medicinal plant Semiliquidambar cathayensis chang leaf and bark at different developmental stage. Metabolites, 15.","DOI":"10.3390\/metabo15020098"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Bian, X., Qiu, Y., Zhao, X., Wei, H., Zhang, Y., Zhang, W., Wang, J., Sun, X., and Sun, X. (2025). Multi-omics dissection of metabolic and transcriptional regulation during Panax ginseng fruit development. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-07221-2"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Li, X., Zhao, Y., He, S., Meng, J., Lu, Y., Shi, H., Liu, C., Hao, B., Tang, Q., and Zhang, S. (2024). Integrated metabolome and transcriptome analyses reveal the molecular mechanism underlying dynamic metabolic processes during taproot development of Panax notoginseng. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-024-04861-8"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.2298\/JSC210507007S","article-title":"HPTLC-based metabolomics for the investigation of metabolic changes during plant development: The case study of Artemisia annua","volume":"87","author":"Trendafilova","year":"2022","journal-title":"J. Serbian Chem. Soc."},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Chu, Z., Xiong, R., Peng, X., Cui, G., Dong, L., and Li, W. (2024). Delineating molecular regulatory of flavonoids indicated by transcriptomic and metabolomics analysis during flower development in Chrysanthemum morifolium \u2018Boju\u2019. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251910261"},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Lin, H., Sun, J., Hu, Z., Cheng, C., Lin, S., Zou, H., and Yan, X. (2022). Variation in glucosinolate accumulation among different sprout and seedling stages of broccoli (Brassica oleracea var. italica)\u201d. Plants, 11.","DOI":"10.3390\/plants11121563"},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Yan, C., Huang, Y., Zhang, S., Cui, L., Jiao, Z., Peng, Z., Luo, X., Liu, Y., and Qiu, Z. (2023). Dynamic profiling of intact glucosinolates in radish by combining UHPLC-HRMS\/MS and UHPLC-QqQ-MS\/MS. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1216682"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"10682","DOI":"10.1038\/s41598-024-60801-4","article-title":"Widely-targeted metabolomics and transcriptomics identify metabolites associated with flowering regulation of Choy Sum","volume":"14","author":"Huang","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Monzillo, F., Della Mura, B., Matarazzo, C., Crescenzi, M.A., Piacente, S., d\u2019Aquino, L., Cozzolino, R., and Montoro, P. (2025). Evolution of Secondary Metabolites in Eruca sativa from the Microgreen to the Reproductive Stage: An Integrative Multi-Platform Metabolomics Approach. Foods, 14.","DOI":"10.3390\/foods14234148"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"e412","DOI":"10.1002\/pld3.412","article-title":"Delineating genetic regulation of cannabinoid biosynthesis during female flower development in Cannabis sativa","volume":"6","author":"Apicella","year":"2022","journal-title":"Plant Direct"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s42238-023-00178-9","article-title":"Glandular trichome development, morphology, and maturation are influenced by plant age and genotype in Cannabis sativa","volume":"5","author":"Punja","year":"2023","journal-title":"J. Cannabis Res."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"122988","DOI":"10.1016\/j.indcrop.2026.122988","article-title":"Flowering stage- and cultivar-specific regulation of cannabinoid biosynthesis in hemp: An integrated transcriptomics and metabolomic analyses","volume":"242","author":"Basnet","year":"2026","journal-title":"Ind. Crops Prod."},{"key":"ref_114","first-page":"e017","article-title":"Integration of metabolome and transcriptome reveals flavonoid metabolic network during the developmental stage of flower buds in Cornus wilsoniana","volume":"4","author":"Cai","year":"2025","journal-title":"Med. Plant Biol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"e17325","DOI":"10.7717\/peerj.17325","article-title":"Metabolite analysis reveals flavonoids accumulation during flower development in Rhododendron pulchrum sweet (Ericaceae)","volume":"12","author":"Yang","year":"2024","journal-title":"PeerJ"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"122657","DOI":"10.1016\/j.indcrop.2026.122657","article-title":"Metabolomics reveals stage-dependent metabolic dynamics associated with quality variation during the development of Albizia julibrissin flower","volume":"240","author":"Cheng","year":"2026","journal-title":"Ind. Crops Prod."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"41718","DOI":"10.1021\/acsomega.3c06043","article-title":"Metabolite Changes in Soybean (Glycine max) Leaves during the Entire Growth Period","volume":"8","author":"Park","year":"2023","journal-title":"ACS Omega"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"111644","DOI":"10.1016\/j.foodres.2022.111644","article-title":"An LC-MS-based metabolomic approach provides insights into the metabolite profiles of Ginkgo biloba L. at different developmental stages and in various organs","volume":"159","author":"Guo","year":"2022","journal-title":"Food Res. Int."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"854","DOI":"10.18016\/ksutarimdoga.vi.1084534","article-title":"The impact of morpho- and onto-genetic variation on essential oil profile of Hypericum heterophyllum Vent., an endemic species in Turkey\u2019s flora","volume":"26","year":"2023","journal-title":"Kahramanmara\u015f S\u00fct\u00e7\u00fc \u0130mam \u00dcniversitesi Tar\u0131m Ve Do\u011fa Derg."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"104429","DOI":"10.1016\/j.bse.2022.104429","article-title":"Ontogenetic changes in phenolic contents and volatile composition of Hypericum androsaemum and Hypericum xylosteifolium","volume":"102","author":"Cirak","year":"2022","journal-title":"Biochem. Syst. Ecol."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"417","DOI":"10.17221\/114\/2021-PSE","article-title":"Effects of harvest stage and diurnal variability on yield and essential oil content in Mentha \u00d7 piperita L","volume":"67","year":"2021","journal-title":"Plant Soil Environ."},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Hazrati, S., Beidaghi, P., Beyraghdar Kashkooli, A., Hosseini, S.J., and Nicola, S. (2022). Effect of harvesting time variations on essential oil yield and composition of Sage (Salvia officinalis). Horticulturae, 8.","DOI":"10.3390\/horticulturae8020149"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"113","DOI":"10.24326\/asphc.2022.3.10","article-title":"The influence of harvesting applied at different stages of plant development on Hyssopus officinalis L. production","volume":"21","author":"Can","year":"2022","journal-title":"Acta Sci. Pol. Hortorum Cultus"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1007\/s11738-025-03815-3","article-title":"Determination of gene expression of some essential oil components and some genes responsible for the synthesis of these components in Mentha species harvested in different phenological periods","volume":"47","author":"Telci","year":"2025","journal-title":"Acta Physiol. Plant."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Dat, N.T., Anh, H.L.T., Huong, L.Q., Anh, N.B.N., Ngoc, N.B., Trung, N.Q., and Minh, T.N. (2026). Developmental-stage-dependent changes in basil essential oil composition. Symmetry, 18.","DOI":"10.3390\/sym18050703"},{"key":"ref_126","first-page":"98","article-title":"Identification of metabolite changes and evaluation of bioactivity during flower development in Clitoria ternatea","volume":"11","author":"Choi","year":"2024","journal-title":"J. Appl. Biol. Chem."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"915","DOI":"10.5650\/jos.ess25113","article-title":"Assessment of quality in essential oil from Magnolia officinalis flos at different developmental stages by anatomy, GC-MS, and chemometric methods","volume":"74","author":"Liu","year":"2025","journal-title":"J. Oleo Sci."},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Bao, W., Shen, Y., and Verdonk, J.C. (2024). Dynamic changes in flavonoids\u2019 accumulation pattern in Tilia miqueliana flowers at different developmental stages based on widely targeted metabolomic analysis. Forests, 15.","DOI":"10.3390\/f15101795"},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Zhou, Y., and Shen, Y. (2025). Integrative transcriptomics and metabolomics reveal the biosynthesis of flavonoid metabolites in Tilia miqueliana Maxim. leaves. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1642949"},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Lin, Z., Deng, K., Chen, F., and Zhao, L. (2025). Integrated multi-omics reveals anthocyanin biosynthesis during jaboticaba fruit peel development. Horticulturae, 11.","DOI":"10.3390\/horticulturae11121515"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"e015","DOI":"10.48130\/frures-0025-0004","article-title":"Integrated transcriptomic and metabolomic analysis reveals light-induced modulation of anthocyanin biosynthesis in Chinese bayberry (Myrica rubra)","volume":"5","author":"Yang","year":"2025","journal-title":"Fruit Res."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"10342","DOI":"10.1038\/s41598-025-93889-3","article-title":"Integrated analysis of transcriptomics and metabolomics of Dendrobium officinale flowers at different developmental stages","volume":"15","author":"Ren","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Li, Y., Wu, Y., Pu, R., Li, X., Bai, T., Li, N., Zhou, Y., and Zhang, J. (2025). Metabolomic and transcriptomic analyses of flavonoid biosynthesis in Dendrobium devonianum flowers. Genes, 16.","DOI":"10.3390\/genes16030264"},{"key":"ref_134","doi-asserted-by":"crossref","unstructured":"Chen, H.Y., Gao, F.L., Guo, Q., Bao, S.N., Li, X., and Khoo, H.E. (2025). Exploration of synthesis of anthocyanins in passion fruit pericarp through metabolomic and transcriptomic analysis. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1658779"},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Pereira, R.C., Ramos, Y.J., and Moreira, D.L. (2025). The eco-evolutionary raison d\u2019\u00eatre of natural products as support for sustainable bioprospecting. Front. Ecol. Evol., 13.","DOI":"10.3389\/fevo.2025.1658630"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"112640","DOI":"10.1016\/j.plantsci.2025.112640","article-title":"LC-MS-based metabolomics revealed dynamic changes of tissue- and developmental stage-specific metabolites in qingke","volume":"359","author":"Xu","year":"2025","journal-title":"Plant Sci."},{"key":"ref_137","doi-asserted-by":"crossref","unstructured":"Tao, L., Long, Q., Chen, J., Zhang, Q., Guo, G., He, F., Cai, H., Geng, J., Song, X., and Zeng, H. (2025). Co-analysis of transcriptome and metabolome reveals flavonoid biosynthesis in Macadamia pericarp across developmental stages. Foods, 14.","DOI":"10.3390\/foods14213618"},{"key":"ref_138","doi-asserted-by":"crossref","unstructured":"Zun, X., and Wang, H. (2025). Metabolite changes during developmental transitions in Adonis amurensis Regel et Radde flowers: Insights from HPLC-MS analysis. PLoS ONE, 20.","DOI":"10.1371\/journal.pone.0321792"},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Ji, X., Ren, J., Zhang, Y., Lang, S., Wang, D., and Song, X. (2021). Integrated analysis of the metabolome and transcriptome on anthocyanin biosynthesis in four developmental stages of Cerasus humilis peel coloration. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222111880"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"e14413","DOI":"10.7717\/peerj.14413","article-title":"Transcriptome and metabolome analyses reveal anthocyanins pathways associated with fruit color changes in plum (Prunus salicina Lindl.)","volume":"10","author":"Chen","year":"2022","journal-title":"PeerJ"},{"key":"ref_141","doi-asserted-by":"crossref","unstructured":"Xuan, Y., Ren, J., Chen, Z., and Shi, D. (2025). Integrated transcriptome and metabolome analyses provide molecular insights into transition of flower color in rose cultivar \u2018Juicy Terrazza\u2019. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06794-2"},{"key":"ref_142","doi-asserted-by":"crossref","unstructured":"Xuan, Y., Ren, J., Chen, Z., and Shi, D. (2025). Integrated metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in relation to color mutation in roses. Biology, 14.","DOI":"10.3390\/biology14101337"},{"key":"ref_143","first-page":"e020","article-title":"Anthocyanin contents and molecular changes in rose petals during the post-anthesis color transition","volume":"4","author":"Kong","year":"2024","journal-title":"Ornam. Plant Res."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.plaphy.2022.09.032","article-title":"Investigation of phenological, primary and secondary metabolites changes during flower developmental of Rosa damascena","volume":"192","author":"Mutlucan","year":"2022","journal-title":"Plant Physiol. Biochem."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Wang, A.H., Zhang, B.H., Ma, C., Wang, J., Kang, C.Y., and Zhang, X.T. (2025). Metabolomic and transcriptomic analyses provide insights into metabolic networks during Fragaria nilgerrensis fruit development and ripening. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-07590-8"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"199","DOI":"10.21273\/JASHS05494-25","article-title":"Targeted metabolomics-based analysis of the dynamics of peel-coloration metabolites during purple hawthorn development","volume":"150","author":"Jing","year":"2025","journal-title":"J. Am. Soc. Hortic. Sci."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"Zhai, Y., Wang, K., Wu, J., Hui, W., Lu, S., Qiu, J., Wu, H., Gong, W., and Wang, J. (2025). Study on the dynamics of fruits color related genes and metabolites during the fruit development of Zanthoxylum bungeanum \u2018Hanyuan\u2019. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06962-4"},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Hu, J., Wang, J., Muhammad, T., Yang, T., Li, N., Yang, H., Yu, Q., and Wang, B. (2024). Integrative analysis of metabolome and transcriptome of carotenoid biosynthesis reveals the mechanism of fruit color change in tomato (Solanum lycopersicum). Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25126493"},{"key":"ref_149","doi-asserted-by":"crossref","unstructured":"Lv, J., Zhang, R., Mo, Y., Zhou, H., Li, M., Wu, R., Cheng, H., Zhang, M., Wang, H., and Hua, W. (2023). Integrative metabolome and transcriptome analyses provide insights into carotenoid variation in different-colored peppers. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms242316563"},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Wang, H., Jia, L., Li, D., Manzoor, M.A., Yan, C., Ding, Q., Wang, Y., Hong, X., Song, T., and Jiang, H. (2025). Transcriptomic and metabolomic analysis reveals the mechanism of H18 pepper color change. Agriculture, 15.","DOI":"10.3390\/agriculture15060655"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"114062","DOI":"10.1016\/j.scienta.2025.114062","article-title":"Metabolomics and transcriptomics analyses provide insights into the dynamic of metabolites and the molecular mechanisms of natural pigment formation of different color-transition types of red pepper (Capsicum)","volume":"342","author":"Wang","year":"2025","journal-title":"Sci. Hortic."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"131850","DOI":"10.1016\/j.foodchem.2021.131850","article-title":"Metabolic shifts during fruit development in pungent and non-pungent peppers","volume":"375","author":"Scossa","year":"2022","journal-title":"Food Chem."},{"key":"ref_153","doi-asserted-by":"crossref","unstructured":"Guo, J., Wang, J., Peng, C., Liu, H., and Shang, J. (2025). Integrated metabolomic and transcriptomic analyses of anthocyanin synthesis during fruit development in Lycium ruthenicum Murr. Biology, 14.","DOI":"10.3390\/biology14111614"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1093\/aob\/mcu222","article-title":"Population divergence in the ontogenetic trajectories of foliar terpenes of a Eucalyptus species","volume":"115","author":"Borzak","year":"2014","journal-title":"Ann. Bot."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Liu, Y., Watanabe, M., Yasukawa, S., Kawamura, Y., Aneklaphakij, C., Fernie, A.R., and Tohge, T. (2021). Cross-species metabolic profiling of floral specialized metabolism facilitates understanding of evolutional aspects of metabolism among Brassicaceae species. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.640141"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1111\/tpj.16220","article-title":"Biochemistry and genetics of floral scent: A historical perspective","volume":"115","author":"Pichersky","year":"2023","journal-title":"Plant J."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1111\/nph.17020","article-title":"WRKY33 interacts with WRKY12 protein to up-regulate RAP2.2 during submergence induced hypoxia response in Arabidopsis thaliana","volume":"229","author":"Tang","year":"2021","journal-title":"New Phytol."},{"key":"ref_158","doi-asserted-by":"crossref","unstructured":"Pei, Z., Huang, Y., Ni, J., Liu, Y., and Yang, Q. (2024). For a colorful life: Recent advances in anthocyanin biosynthesis during leaf senescence. Biology, 13.","DOI":"10.3390\/biology13050329"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1146\/annurev-arplant-083123-082752","article-title":"Environmental and biological drivers of root exudation","volume":"76","author":"Robert","year":"2025","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/j.jgg.2023.10.004","article-title":"Two diversities meet in the rhizosphere: Root specialized metabolites and microbiome","volume":"51","author":"Wang","year":"2024","journal-title":"J. Genet. Genom."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1146\/annurev.ecolsys.31.1.565","article-title":"The evolutionary ecology of tolerance to consumer damage","volume":"31","author":"Stowe","year":"2000","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1146\/annurev.ecolsys.28.1.243","article-title":"Preserving the information content of species: Genetic diversity, phylogeny, and conservation","volume":"28","author":"Crozier","year":"1997","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"2141","DOI":"10.1126\/science.291.5511.2141","article-title":"Defensive function of herbivore-induced plant volatile emissions in nature","volume":"291","author":"Kessler","year":"2001","journal-title":"Science"},{"key":"ref_164","unstructured":"Rosenthal, G.A., and Janzen, D.H. (1979). The distribution of secondary compounds within plants. Herbivores: Their Interaction with Secondary Plant Metabolites, Academic Press."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1086\/367580","article-title":"Out of the quagmire of plant defense hypotheses","volume":"78","author":"Stamp","year":"2003","journal-title":"Q. Rev. Biol."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1146\/annurev-arplant-042916-040856","article-title":"Trade-offs between plant growth and defense against insect herbivory: An emerging mechanistic synthesis","volume":"68","author":"Agrawal","year":"2017","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1086\/417659","article-title":"The dilemma of plants: To grow or defend","volume":"67","author":"Herms","year":"1992","journal-title":"Q. Rev. Biol."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1093\/mp\/ssu049","article-title":"Growth-defense tradeoffs in plants: A balancing act to optimize fitness","volume":"7","author":"Huot","year":"2014","journal-title":"Mol. Plant"},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1111\/1365-2435.13425","article-title":"Chemical defense over decadal scales: Ontogenetic allocation trajectories and consequences for fitness in a foundation tree species","volume":"33","author":"Cope","year":"2019","journal-title":"Funct. Ecol."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1111\/1365-2435.13854","article-title":"Exciting discoveries in animal signalling and sexual dichromatism","volume":"35","author":"Grether","year":"2021","journal-title":"Funct. Ecol."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1146\/annurev.ecolsys.38.091206.095601","article-title":"Wake up and smell the roses: The ecology and evolution of floral scent","volume":"39","author":"Raguso","year":"2008","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1111\/j.1365-2435.2009.01643.x","article-title":"Floral scent in a whole-plant context: Moving beyond pollinator attraction","volume":"23","author":"Raguso","year":"2009","journal-title":"Funct. Ecol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1139\/Z10-031","article-title":"The chemical ecology and evolution of bee\u2013flower interactions: A review and perspectives","volume":"88","author":"Vereecken","year":"2010","journal-title":"Can. J. Zool."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.cois.2016.02.012","article-title":"The behavioral ecology of variation in social insects","volume":"15","author":"Jandt","year":"2016","journal-title":"Curr. Opin. Insect Sci."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1111\/een.13241","article-title":"Population and movement ecology of two life-history contrasting dung beetle species in a tropical human-modified landscape","volume":"48","author":"Barretto","year":"2023","journal-title":"Ecol. Entomol."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.tree.2004.08.003","article-title":"How plant-animal interactions signal new insights in communication","volume":"19","author":"Schaefer","year":"2004","journal-title":"Trends Ecol. Evol."},{"key":"ref_177","doi-asserted-by":"crossref","unstructured":"Nevo, O., Valenta, K., Helman, A., Ganzhorn, J.U., and Ayasse, M. (2022). Fruit scent as an honest signal for fruit quality. BMC Ecol. Evol., 22.","DOI":"10.1186\/s12862-022-02064-z"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1186\/s40168-021-01118-6","article-title":"Plant developmental stage drives the differentiation in ecological role of the plant microbiome","volume":"9","author":"Xiong","year":"2021","journal-title":"Microbiome"},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/nature16192","article-title":"Functional overlap of the Arabidopsis leaf and root microbiota","volume":"528","author":"Bai","year":"2015","journal-title":"Nature"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"e09213","DOI":"10.1111\/oik.09213","article-title":"Ontogenetic changes in root traits and root-associated fungal community composition in a heteroblastic epiphytic bromeliad","volume":"2023","author":"Leroy","year":"2023","journal-title":"Oikos"},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"2730","DOI":"10.1111\/1365-2435.13221","article-title":"Ontogenetic shifts in plant ecological strategies","volume":"32","author":"Dayrell","year":"2018","journal-title":"Funct. Ecol."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.tplants.2022.02.002","article-title":"A rulebook for peptide control of legume\u2013microbe endosymbiosis","volume":"27","author":"Roy","year":"2022","journal-title":"Trends Plant Sci."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1111\/1365-2435.13789","article-title":"Body size and shape responses to warming and resource competition","volume":"35","author":"Tan","year":"2021","journal-title":"Funct. Ecol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1111\/j.1469-185X.1977.tb01347.x","article-title":"The maintenance of species-richness in plant communities: The importance of the regeneration niche","volume":"52","author":"Grubb","year":"1977","journal-title":"Biol. Rev."},{"key":"ref_185","doi-asserted-by":"crossref","unstructured":"Desurmont, G.A., Laplanche, D., Schiestl, F.P., and Turlings, T.C.J. (2015). Floral volatiles interfere with plant attraction of parasitoids: Ontogeny-dependent infochemical dynamics in Brassica rapa. BMC Ecol., 15.","DOI":"10.1186\/s12898-015-0047-7"},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1093\/aob\/mcac087","article-title":"Characterization, costs, cues and future perspectives of phenotypic plasticity","volume":"130","author":"Schneider","year":"2022","journal-title":"Ann. Bot."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"dev203026","DOI":"10.1242\/dev.203026","article-title":"Analysis of auxin responses in the fern Ceratopteris richardii identifies the developmental phase as a major determinant for response properties","volume":"151","author":"Woudenberg","year":"2024","journal-title":"Development"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1111\/1365-2435.13435","article-title":"Shifts in woody plant defence syndromes during leaf development","volume":"33","author":"Barton","year":"2019","journal-title":"Funct. Ecol."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1038\/s41598-017-04314-3","article-title":"Interactive effects of plant neighbourhood and ontogeny on insect herbivory and plant defensive traits","volume":"7","author":"Moreira","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1002\/pca.3300","article-title":"A multiplex approach of MS, 1D- and 2D-NMR metabolomics in plant ontogeny: A case study on Clusia minor L. organs (leaf, flower, fruit, and seed)","volume":"35","author":"Tavares","year":"2024","journal-title":"Phytochem. Anal."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1111\/plb.13704","article-title":"Ontogeny and organ-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two Solanum dulcamara leaf chemotypes","volume":"27","author":"Anaia","year":"2025","journal-title":"Plant Biol."},{"key":"ref_192","doi-asserted-by":"crossref","unstructured":"Muhlemann, J.K., Maeda, H., Chang, C.Y., San Miguel, P., Baxter, I., Cooper, B., Perera, M.A., Nikolau, B.J., Vitek, O., and Morgan, J.A. (2012). Developmental changes in the metabolic network of snapdragon flower. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0040381"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"uhad048","DOI":"10.1093\/hr\/uhad048","article-title":"A molecular phenology scale of grape berry development","volume":"10","author":"Tornielli","year":"2023","journal-title":"Hortic. Res."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"e8545","DOI":"10.1002\/ece3.8545","article-title":"A domestic plant differs from its wild relative along multiple axes of within-plant trait variability and diversity","volume":"12","author":"Robinson","year":"2022","journal-title":"Ecol. Evol."},{"key":"ref_195","doi-asserted-by":"crossref","unstructured":"Al-Hakeem, M.J., Salih, A.A.A., and Alqahtani, A.S. (2025). The role of statistics in advancing nitric oxide research in plant biology: From data analysis to mechanistic insights. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1597030"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1023\/A:1013713905833","article-title":"Metabolomics\u2014The link between genotypes and phenotypes","volume":"48","author":"Fiehn","year":"2002","journal-title":"Plant Mol. Biol."},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"30.2.1","DOI":"10.1002\/0471142727.mb3002s98","article-title":"Targeted metabolomics","volume":"98","author":"Roberts","year":"2012","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.1038\/s41596-020-0341-5","article-title":"Development of a plasma pseudotargeted metabolomics method based on ultra-high-performance liquid chromatography-mass spectrometry","volume":"15","author":"Zheng","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nrm.2016.25","article-title":"Metabolomics: Beyond biomarkers and towards mechanisms","volume":"17","author":"Johnson","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1038\/nprot.2007.95","article-title":"Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry","volume":"2","author":"Moco","year":"2007","journal-title":"Nat. Protoc."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1021\/acs.analchem.0c04371","article-title":"Combined nuclear magnetic resonance spectroscopy and mass spectrometry approaches for metabolomics","volume":"93","author":"Letertre","year":"2021","journal-title":"Anal. Chem."},{"key":"ref_202","first-page":"15","article-title":"Untargeted metabolomics applications in biomarker discovery","volume":"7","author":"Nalbantoglu","year":"2019","journal-title":"Curr. Metabolomics"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/nprot.2011.335","article-title":"Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry","volume":"6","author":"Dunn","year":"2011","journal-title":"Nat. Protoc."},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1590\/sajs.2013\/20120005","article-title":"Plant metabolomics: A new frontier in phytochemical analysis","volume":"109","author":"Tugizimana","year":"2013","journal-title":"S. Afr. J. Sci."},{"key":"ref_205","doi-asserted-by":"crossref","unstructured":"K\u0131l\u0131n\u00e7, H., Ligor, M., Ligor, T., and Buszewski, B. (2023). LC-MS and NMR based plant metabolomics. Metabolites, 13.","DOI":"10.3390\/metabo13101051"},{"key":"ref_206","first-page":"389","article-title":"LC-MS applications in plant secondary metabolism","volume":"13","author":"Serag","year":"2023","journal-title":"J. Pharm. Anal."},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.copbio.2016.08.001","article-title":"The future of NMR-based metabolomics","volume":"43","author":"Markley","year":"2017","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1007\/s42994-024-00194-0","article-title":"Plant metabolomics: Applications and challenges in the era of multi-omics big data","volume":"6","author":"Hao","year":"2025","journal-title":"aBIOTECH"},{"key":"ref_209","doi-asserted-by":"crossref","unstructured":"Myers, R.J., Tretter, Z.M., Daffron, A.G., Fritschi, E.X., Santos, W.T., Foster, M.L., Klotz, M., Stafford, K.M., Kasch, C., and Taylor, T.J. (2025). Spatially resolved plant metabolomics. Metabolites, 15.","DOI":"10.3390\/metabo15080539"},{"key":"ref_210","doi-asserted-by":"crossref","unstructured":"Patel, M.K., Pandey, S., Kumar, M., Haque, M.I., Pal, S., and Yadav, N.S. (2021). Plants metabolome study: Emerging tools and techniques. Plants, 10.","DOI":"10.20944\/preprints202107.0193.v1"},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"104481","DOI":"10.1016\/j.tifs.2024.104481","article-title":"Metabolomics and chemometrics: The next-generation analytical toolkit for the evaluation of food quality and authenticity","volume":"147","author":"Becchi","year":"2024","journal-title":"Trends Food Sci. Technol."},{"key":"ref_212","first-page":"92","article-title":"Multivariate analysis in metabolomics","volume":"1","author":"Worley","year":"2013","journal-title":"Curr. Metabolomics"},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"13738","DOI":"10.1073\/pnas.1608041113","article-title":"Topic modeling for untargeted substructure exploration in metabolomics","volume":"113","author":"Wandy","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"e70001","DOI":"10.1002\/aps3.70001","article-title":"Analysis of plant metabolomics data using identification-free approaches","volume":"13","author":"Yuan","year":"2025","journal-title":"Appl. Plant Sci."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1038\/s41592-020-0933-6","article-title":"Feature-based molecular networking in the GNPS analysis environment","volume":"17","author":"Nothias","year":"2020","journal-title":"Nat. Methods"},{"key":"ref_217","doi-asserted-by":"crossref","unstructured":"Qin, G.F., Zhang, X., Zhu, F., Huo, Z.Q., Yao, Q.Q., Feng, Q., Liu, Z., Zhang, G.M., Yao, J.C., and Liang, H.B. (2023). MS\/MS-based molecular networking: An efficient approach for natural products dereplication. Molecules, 28.","DOI":"10.3390\/molecules28010157"},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"2795","DOI":"10.1021\/acs.jnatprod.1c00399","article-title":"NPClassifier: A deep neural network-based structural classification tool for natural products","volume":"84","author":"Kim","year":"2021","journal-title":"J. Nat. Prod."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"3832","DOI":"10.1038\/s41467-021-23953-9","article-title":"Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment","volume":"12","author":"Schmid","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_220","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_221","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1111\/j.1365-313X.2007.03293.x","article-title":"Data integration in plant biology: The O2PLS method for combined modeling of transcript and metabolite data","volume":"52","author":"Eriksson","year":"2007","journal-title":"Plant J."},{"key":"ref_222","doi-asserted-by":"crossref","unstructured":"Jamil, I.N., Remali, J., Azizan, K.A., Nor Muhammad, N.A., Arita, M., Goh, H.H., and Aizat, W.M. (2020). Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.00944"},{"key":"ref_223","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_224","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1007\/s11101-015-9416-2","article-title":"The potential of mass spectrometry imaging in plant metabolomics: A review","volume":"15","author":"Heyman","year":"2016","journal-title":"Phytochem. Rev."},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/jxb\/erad423","article-title":"Imaging plant metabolism in situ","volume":"75","author":"Horn","year":"2024","journal-title":"J. Exp. Bot."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.tplants.2025.10.005","article-title":"Advances in plant spatial multi-omics data analysis","volume":"31","author":"Yao","year":"2025","journal-title":"Trends Plant Sci."},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/S0031-9422(02)00708-2","article-title":"Plant metabolomics: Large-scale phytochemistry in the functional genomics era","volume":"62","author":"Sumner","year":"2003","journal-title":"Phytochemistry"},{"key":"ref_228","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1111\/j.1469-8137.2005.01632.x","article-title":"Plant metabolomics: From holistic hope, to hype, to hot topic","volume":"169","author":"Hall","year":"2006","journal-title":"New Phytol."},{"key":"ref_229","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/ele.13422","article-title":"The many dimensions of phytochemical diversity: Linking theory to practice","volume":"23","author":"Wetzel","year":"2020","journal-title":"Ecol. Lett."},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"1893","DOI":"10.1104\/pp.104.049981","article-title":"Biochemistry of plant volatiles","volume":"135","author":"Dudareva","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1086\/286069","article-title":"Secondary metabolites of fleshy vertebrate-dispersed fruits: Adaptive hypotheses and implications for seed dispersal","volume":"150","author":"Cipollini","year":"1997","journal-title":"Am. Nat."},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"S170","DOI":"10.1105\/tpc.019158","article-title":"Genetic regulation of fruit development and ripening","volume":"16","author":"Giovannoni","year":"2004","journal-title":"Plant Cell"},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1146\/annurev-arplant-050312-120057","article-title":"Fruit development and ripening","volume":"64","author":"Seymour","year":"2013","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1146\/annurev-genet-110410-132507","article-title":"Genetics and control of tomato fruit ripening and quality attributes","volume":"45","author":"Klee","year":"2011","journal-title":"Annu. Rev. Genet."},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst. Tech. J."},{"key":"ref_236","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/163688a0","article-title":"Measurement of diversity","volume":"163","author":"Simpson","year":"1949","journal-title":"Nature"},{"key":"ref_237","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0022-5193(66)90013-0","article-title":"The measurement of diversity in different types of biological collections","volume":"13","author":"Pielou","year":"1966","journal-title":"J. Theor. Biol."},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0040-5809(82)90004-1","article-title":"Diversity and dissimilarity coefficients: A unified approach","volume":"21","author":"Rao","year":"1982","journal-title":"Theor. Popul. Biol."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/S1360-1385(00)01797-0","article-title":"Phenotypic plasticity for plant development, function and life history","volume":"5","author":"Sultan","year":"2000","journal-title":"Trends Plant Sci."},{"key":"ref_240","doi-asserted-by":"crossref","unstructured":"Pigliucci, M. (2001). Phenotypic Plasticity: Beyond Nature and Nurture, Johns Hopkins University Press.","DOI":"10.56021\/9780801867880"},{"key":"ref_241","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1111\/j.1365-2745.2006.01176.x","article-title":"Quantitative estimation of phenotypic plasticity: Bridging the gap between the evolutionary concept and its ecological applications","volume":"94","author":"Valladares","year":"2006","journal-title":"J. Ecol."},{"key":"ref_242","unstructured":"Jolliffe, I.T. (2002). Principal Component Analysis, Springer. [2nd ed.]."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1055\/s-0029-1185450","article-title":"Quality control of herbal material and phytopharmaceuticals with MS and NMR based metabolic fingerprinting","volume":"75","author":"Maltese","year":"2009","journal-title":"Planta Medica"},{"key":"ref_244","first-page":"1934578X0900401019","article-title":"MS-based plant metabolomic approaches for biomarker discovery","volume":"4","author":"Wolfender","year":"2009","journal-title":"Nat. Prod. Commun."},{"key":"ref_245","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.plaphy.2020.01.006","article-title":"The effect of developmental and environmental factors on secondary metabolites in medicinal plants","volume":"148","author":"Li","year":"2020","journal-title":"Plant Physiol. Biochem."},{"key":"ref_246","doi-asserted-by":"crossref","unstructured":"Wang, H., Chen, Y., Wang, L., Liu, Q., Yang, S., and Wang, C. (2023). Advancing herbal medicine: Enhancing product quality and safety through robust quality control practices. Front. Pharmacol., 14.","DOI":"10.3389\/fphar.2023.1265178"},{"key":"ref_247","doi-asserted-by":"crossref","first-page":"109336","DOI":"10.1016\/j.scienta.2020.109336","article-title":"Optimization of harvest date according to the volatile composition of Mediterranean aromatic herbs at different vegetative stages","volume":"267","year":"2020","journal-title":"Sci. Hortic."},{"key":"ref_248","doi-asserted-by":"crossref","first-page":"2853","DOI":"10.1002\/fsn3.2241","article-title":"Effects of different harvesting times and processing methods on the quality of cultivated Fritillaria cirrhosa D. Don","volume":"9","author":"Ma","year":"2021","journal-title":"Food Sci. Nutr."},{"key":"ref_249","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.phytochem.2010.02.001","article-title":"Metabolic classification of South American Ilex species by NMR-based metabolomics","volume":"71","author":"Kim","year":"2010","journal-title":"Phytochemistry"},{"key":"ref_250","doi-asserted-by":"crossref","unstructured":"Yeshi, K., Crayn, D., Ritmejeryt\u0117, E., and Wangchuk, P. (2022). Plant secondary metabolites produced in response to abiotic stresses has potential application in pharmaceutical product development. Molecules, 27.","DOI":"10.3390\/molecules27010313"},{"key":"ref_251","doi-asserted-by":"crossref","unstructured":"Spaggiari, C., Righetti, L., Spadini, C., Annunziato, G., Nsanzurwimo, A., Cabassi, C.S., Bruni, R., and Costantino, G. (2023). Metabolite profiling and bioactivities of leaves, stems, and flowers of Rumex usambarensis (dammer) dammer, a traditional African medicinal plant. Plants, 12.","DOI":"10.3390\/plants12030482"},{"key":"ref_252","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.phytochem.2019.02.013","article-title":"Plant chemophenetics\u2014A new term for plant chemosystematics\/plant chemotaxonomy in the macro-molecular era","volume":"163","author":"Zidorn","year":"2019","journal-title":"Phytochemistry"},{"key":"ref_253","doi-asserted-by":"crossref","unstructured":"Fu, J., Liu, Y., Gou, W., Liu, M., Zhang, N., Si, Q., and Shang, H. (2025). Metabolomic and Transcriptomic Analyses Reveal Changes in Active Components During the Growth and Development of Comfrey (Symphytum officinale L.). Plants, 14.","DOI":"10.3390\/plants14142088"},{"key":"ref_254","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1111\/plb.13763","article-title":"Intraspecific and intra-individual chemodiversity and phenotypic integration of terpenes across plant parts and development stages in an aromatic plant","volume":"27","author":"Ziaja","year":"2025","journal-title":"Plant Biol."},{"key":"ref_255","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev-ecolsys-110617-062406","article-title":"Plant secondary metabolite diversity and species interactions","volume":"49","author":"Kessler","year":"2018","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref_256","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1042\/ETLS20210248","article-title":"The ease and complexity of identifying and using specialized metabolites for crop engineering","volume":"6","author":"Muhich","year":"2022","journal-title":"Emerg. Top. Life Sci."},{"key":"ref_257","doi-asserted-by":"crossref","first-page":"108735","DOI":"10.1016\/j.plaphy.2024.108735","article-title":"Harvest time optimization for medicinal and aromatic plant secondary metabolites","volume":"212","author":"Hazrati","year":"2024","journal-title":"Plant Physiol. Biochem."},{"key":"ref_258","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1039\/D5NP00040H","article-title":"Cultivar to chemotype: Characterizing complex botanicals with mass spectrometry metabolomics","volume":"43","author":"Kellogg","year":"2025","journal-title":"Nat. Prod. Rep."},{"key":"ref_259","doi-asserted-by":"crossref","unstructured":"Zhang, C., Zhong, X., Bao, S., Urtnasan, M., and Li, M. (2025). Main factors affecting the efficacy of medicinal plants during the cultivation process. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1634926"},{"key":"ref_260","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1002\/cfg.496","article-title":"Plant Ontology: A controlled vocabulary of plant structures and growth stages","volume":"6","author":"Jaiswal","year":"2005","journal-title":"Comp. Funct. Genom."},{"key":"ref_261","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkm908","article-title":"The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations","volume":"36","author":"Avraham","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_262","doi-asserted-by":"crossref","unstructured":"Walls, R.L., Cooper, L., Elser, J., Gandolfo, M.A., Mungall, C.J., Smith, B., Stevenson, D.W., and Jaiswal, P. (2019). The Plant Ontology facilitates comparisons of plant development stages across species. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.00631"},{"key":"ref_263","doi-asserted-by":"crossref","first-page":"5417","DOI":"10.1093\/jxb\/erv271","article-title":"Towards recommendations for metadata and data handling in plant phenotyping","volume":"66","author":"Krajewski","year":"2015","journal-title":"J. Exp. Bot."},{"key":"ref_264","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1111\/nph.16544","article-title":"Enabling reusability of plant phenomic datasets with MIAPPE 1.1","volume":"227","author":"Papoutsoglou","year":"2020","journal-title":"New Phytol."},{"key":"ref_265","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/s11306-007-0068-0","article-title":"Minimum reporting standards for plant biology context information in metabolomic studies","volume":"3","author":"Fiehn","year":"2007","journal-title":"Metabolomics"},{"key":"ref_266","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s11306-007-0082-2","article-title":"Proposed minimum reporting standards for chemical analysis","volume":"3","author":"Sumner","year":"2007","journal-title":"Metabolomics"},{"key":"ref_267","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s11306-007-0081-3","article-title":"Proposed minimum reporting standards for data analysis in metabolomics","volume":"3","author":"Goodacre","year":"2007","journal-title":"Metabolomics"},{"key":"ref_268","doi-asserted-by":"crossref","first-page":"bat029","DOI":"10.1093\/database\/bat029","article-title":"The MetaboLights repository: Curation challenges in metabolomics","volume":"2013","author":"Salek","year":"2013","journal-title":"Database"},{"key":"ref_269","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref_270","doi-asserted-by":"crossref","unstructured":"Hong, J., Yang, L., Zhang, D., and Shi, J. (2016). Plant metabolomics: An indispensable system biology tool for plant science. Int. J. Mol. Sci., 17.","DOI":"10.3390\/ijms17060767"},{"key":"ref_271","doi-asserted-by":"crossref","unstructured":"Wang, M., Zhang, S., Li, R., and Zhao, Q. (2024). Unraveling the specialized metabolic pathways in medicinal plant genomes: A review. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1459533"},{"key":"ref_272","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1111\/j.1365-313X.2011.04640.x","article-title":"High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions","volume":"67","author":"Caldana","year":"2011","journal-title":"Plant J."},{"key":"ref_273","doi-asserted-by":"crossref","first-page":"5619","DOI":"10.1093\/jxb\/eru322","article-title":"A network perspective on nitrogen metabolism from model to crop plants using integrated \u2018omics\u2019 approaches","volume":"65","author":"Fukushima","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_274","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.tig.2008.10.010","article-title":"Metabolomics-assisted breeding: A viable option for crop improvement","volume":"25","author":"Fernie","year":"2009","journal-title":"Trends Genet."},{"key":"ref_275","doi-asserted-by":"crossref","unstructured":"Salem, M.A., Perez de Souza, L., Serag, A., Fernie, A.R., Farag, M.A., Ezzat, S.M., and Alseekh, S. (2020). Metabolomics in the context of plant natural products research: From sample preparation to metabolite analysis. Metabolites, 10.","DOI":"10.3390\/metabo10010037"},{"key":"ref_276","first-page":"D440","article-title":"MetaboLights: A resource evolving in response to the needs of its scientific community","volume":"48","author":"Haug","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_277","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/s11306-021-01796-1","article-title":"New software tools, databases, and resources in metabolomics: Updates from 2020","volume":"17","author":"Misra","year":"2021","journal-title":"Metabolomics"},{"key":"ref_278","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.molp.2022.09.007","article-title":"Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives","volume":"16","author":"Shen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_279","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1039\/D4NP00008K","article-title":"Empowering natural product science with AI: Leveraging multimodal data and knowledge graphs","volume":"42","author":"Meijer","year":"2025","journal-title":"Nat. Prod. Rep."},{"key":"ref_280","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/s11306-022-01963-y","article-title":"Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools","volume":"18","author":"Mildau","year":"2022","journal-title":"Metabolomics"},{"key":"ref_281","doi-asserted-by":"crossref","first-page":"4103","DOI":"10.1016\/j.apsb.2025.12.030","article-title":"Revolutionizing drug discovery from natural products: The roles of artificial intelligence and multi-omics in accelerating innovation","volume":"16","author":"Wang","year":"2025","journal-title":"Acta Pharm. Sin. B"},{"key":"ref_282","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1111\/j.1365-2648.2005.03621.x","article-title":"The integrative review: Updated methodology","volume":"52","author":"Whittemore","year":"2005","journal-title":"J. Adv. Nurs."},{"key":"ref_283","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1177\/1534484305278283","article-title":"Writing integrative literature reviews: Guidelines and examples","volume":"4","author":"Torraco","year":"2005","journal-title":"Hum. Resour. Dev. Rev."},{"key":"ref_284","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1111\/j.1471-1842.2009.00848.x","article-title":"A typology of reviews: An analysis of 14 review types and associated methodologies","volume":"26","author":"Grant","year":"2009","journal-title":"Health Inf. Libr. J."},{"key":"ref_285","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.jbusres.2019.07.039","article-title":"Literature review as a research methodology: An overview and guidelines","volume":"104","author":"Snyder","year":"2019","journal-title":"J. Bus. Res."},{"key":"ref_286","doi-asserted-by":"crossref","unstructured":"Noviana, E., Indrayanto, G., and Rohman, A. (2022). Advances in fingerprint analysis for standardization and quality control of herbal medicines. Front. Pharmacol., 13.","DOI":"10.3389\/fphar.2022.853023"},{"key":"ref_287","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1111\/nph.70496","article-title":"Exploring the importance of aromatic plants\u2019 extrafloral volatiles for pollinator attraction","volume":"248","author":"Kantsa","year":"2025","journal-title":"New Phytol."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2756\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T04:19:40Z","timestamp":1789100380000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2756"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":287,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182756"],"URL":"https:\/\/doi.org\/10.3390\/plants15182756","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]}}}