Metabolomics and Transcription Profiling of Pumpkin Fruit Reveals Enhanced Bioactive Flavonoids and Coumarins in Giant Pumpkin (Cucurbita maxima)

Abstract

Atlantic giant (AG, Cucurbita maxima) is a type of giant pumpkin in the Cucurbitaceae family and has the world's largest fruit. AG possesses excellent ornamental and economic value due to its well-known large fruit. However, giant pumpkins are usually thrown away after viewing, thus generating a waste of resources. To explore the additional value of giant pumpkins, a metabolome assay was performed between AG and Hubbard (a small fruit pumpkin) fruits. We found that bioactive compounds, especially flavonoids (including 8-prenylnaringenin, tetrahydrocurcumin, galangin, and acacetin) and coumarins (including coumarin, umbelliferone, 4-coumaryl alcohol, and coumaryl acetate), with extensive antioxidant and pharmacological functions, showed higher accumulation in AG fruit than in Hubbard fruits. Comparative transcriptomics of the two pumpkin fruits indicated that the differentially expressed genes (DEGs) encoding PAL, C4H, 4CL, CSE, HCT, CAD, and CCoAOMT were relatively highly expressed, which promoted an increased accumulation of the identified flavonoids and coumarins in giant pumpkins. In addition, the construction of a co-expression network and cis-element analysis of the promoter demonstrated that differentially expressed MYB, bHLH, AP2, and WRKY transcription factors might play vital roles in regulating the expression of DEGs involved in the biosynthesis of several flavonoids and coumarins. Our current results provide new insights into the accumulation of active compounds in giant pumpkins.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress

“…Three root samples were collected from each of the following groups: blanks, mild waterlogging (BF-1), moderate waterlogging (CF-1), and heavy waterlogging (SF-1) for transcriptome sequencing, yielding a total of 12 qualified libraries, from which clean reads were obtained by eliminating low-quality reads, resulting in approximately 76. 25 Gb of clean data. The clean data of each sample exceeded 5.73 Gb, with Q30 bases accounting for over 91.21%.…”

“…Transcriptome assembly was performed using Trinity [ 21 ], with default parameters except for the “min_kmer_cov” parameter, which was set to 2. Gene functions were annotated by referencing several databases including NR (NCBI non-redundant protein sequences) [ 22 ], Pfam (Protein family) [ 23 ], KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins) [ 24 ], Swiss-Prot (a manually annotated and reviewed protein sequence database) [ 25 ], KEGG (Kyoto Encyclopedia of Genes and Genomes) [ 26 ], and GO (Gene Ontology) [ 27 ]. Intergroup DEGs were analyzed for BF-1, CF-1, MF-1, and SF-1 using the DESeq R package (1.10.1) [ 28 ], and DEGs were functionally clustered via the KEGG pathway and GO [ 29 ].…”

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight into Molecular Mechanisms of Flavonoid Metabolites Biosynthesis in Styphnolobium japonicum

“…Co-expression-network prediction and cis-element analysis with the promoters of flavonoid biosynthesis-related structural genes suggested that WRKY and AP2 TFs may play vital roles in regulating flavonoid biosynthesis [ 71 ]. Transcriptomic and spatiotemporal expression characteristic analysis in Freesia indicated that the expression patterns of selected WRKY and AP2 TF genes were consistent with flavonoid accumulation in the petals, suggesting their involvement in the regulation of flavonoid metabolism [ 72 ].…”