Chemical Ontogeny in Plants: Developmental Dynamics of Specialized Metabolism and Implications for Ecology, Quality Control, and Bioprospecting

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.