Identifying the discrepancies between cultivated tea and its wild relatives, especially in terms of their chemical compositions, is important in exploitation of specific germplasms. This study systematically investigated the phylogenetic relationships, morphological traits, and metabolite profiles of 27 typical tea accessions. Results showed that 84,797 high-quality single nucleotide polymorphisms classified the sampled tea accessions into two groups, namely, Camellia sinensis (L.) O. Kuntze (CS) and its close relatives (CR), most of which were supported by morphological evidence. Targeted metabolomic analyses absolutely quantified 51 characteristic metabolites. Among these metabolites, two tetragalloyled hydrolyzable tannins and four flavonol trisaccharide glycosides accumulated in low amounts in CS and CR, respectively. Furthermore, the notable discrepancy in chemical composition was validated by the metabolite profiles of 114 tea accessions. Overall, this study showed the diversification of Sect. Thea plants regarding the genetic, morphological, and chemical characteristics, leading to a better understanding of wild tea plants. All...

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