Genetic, morphological, and chemical discrepancies between Camellia sinensis (L.) O. Kuntze and its close relatives

•A systematical study on genetics, morphology, and chemistry diversification of tea.•84,797 SNPs classifies 27 tea accessions into CS and CR groups.•Quantification of 51 characteristic metabolites confirmed the phylogenetic structure.•HTs and flavonol glycosides are the metabolite signatures between CS and CR.