Differential tissue distribution of metabolites in Jacobaea vulgaris, Jacobaea aquatica and their crosses

► We compared the metabolomic profiles of epidermis and mesophyll in plants of the genus Jacobaea. ► The epidermis contained more phenylpropanoids, specifically chlorogenic acid. ► The mesophyll contained more pyrrolizidine alkaloids, specifically jacobine and jaconine. ► The observed distribution pattern was consistent over different genotypes. ► The result of tissue specific defense may have a major impact on host plant resistance.