Expression profiling and putative biosynthetic network of flavonoids by global analysis with simplified omics data elucidating the large potential of Akebia trifoliata as an herbal industrial plant

Akebia trifoliata has been under development as a multipurpose industrial plant for pharmaceutical, cosmetic and other biological applications, with flavonoids as the most interesting secondary metabolites. However, the accumulation dynamics and genetic regulatory network of flavonoids in A. trifoliata fruit have not been completely revealed. Here, we first annotated 258 enzyme-encoding genes (EGs) in the flavonoid biosynthetic pathway and a total of 1602 transcription factors (TFs) from the A. trifoliata reference genome, extracted the corresponding expression data from the available transcriptome data, and identified a total of 143 flavonoids, consisting of 29 aglycones and 114 derivatives, from the published metabolome. Second, we screened 54 EGs and 58 TFs by weighted gene coexpression network analysis (WGCNA) and found 11 nodal aglycones consisting of nine detected aglycones and two putative aglycones. Finally, we identified 10 key EGs and 4 key TFs based on both expression difference and expression network analysis, with four EGs (ANS1, F3H1, F3'H3 and DFR2) assigned to the subpathway of flavonoid synthesis (ko00941) and four TFs (MYB66, MYB5, bHLH71, TALE8) playing dominant regulatory roles. In conclusion, Ko00941 could be an important process regulating flavonoid biosynthesis in A. trifoliata fruit, mainly by modifying carbon rings, and DFR2 could play the most important role. In addition, A. trifoliata fruit could be an ideal system for investigating various secondary metabolites, especially at the young or ripe stage, and it could also be a new raw resource for meeting various demands for flavonoids.