Integrated metabolomic and transcriptomic analyses elucidates the molecular mechanisms underlying cucurbitacin accumulation and bitterness development in Luffa fruits

The fruits of Luffa in the Cucurbitaceae family are characterized by a bitter taste, which is mainly attributed to cucurbitacin. However, the types of cucurbitacins related to bitterness and the molecular mechanism of cucurbitacin accumulation during Luffa fruit growth and development remain largely unclear. Here, we identified a total of 633 metabolites in Luffa, including alkaloids, flavonoids, and terpenoids, with 364 key metabolites showing significant differences between bitter and non-bitter varieties. Cucurbitacins B and D were significantly more abundant in bitter Luffa and showed an upward trend from non-bitter to extra-bitter varieties. Transcriptome analysis revealed 25,577 differentially expressed genes (DEGs) in these Luffa varieties, including the upregulation of terpenoid biosynthetic pathways in bitter fruits. Integrative metabolite profiling and transcriptome analyses showed that LaCBS(Luffa cucurbitadienol synthase), encoding cucurbitadienol synthase, is a hub gene for the first committed step in cucurbitacin biosynthesis, located within gene clusters comprising LaP450s(Luffa cytochrome P450s) and LaACT(Luffa acetyltransferase). In addition, two LaCBS genes were located within two gene clusters, alongside LaP450s and LaACT, in the interspecific hybrid of Luffa. A total of 746 DEGs were identified as transcription factors, including 103 LabHLH family members; two LabHLHs were positively correlated with LaCBS and LaACT. Heat and abscisic acid stress activated the cucurbitacin biosynthetic pathway. These findings help to elucidate the molecular mechanism of cucurbitacin biosynthesis in bitter Luffa fruits.