Unveiling molecular mechanisms of pigment synthesis in gardenia (Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis

•A combined study employing transcriptomics and metabolomics was carried out in the premature and mature developmental phases of Gardenia jasminoides Ellis fruits to uncover the molecular mechanisms underlying pigment synthesis.•The transcriptomics analysis effectively detected approximately 3,914 genes showing differential expression, linked to crucial biological processes such as photosynthesis, chlorophyll biosynthesis and pathways involving protein-chromophore linkage.•Metabolomics analysis using Ultra Performance Liquid Chromatography and mass spectrometry (UPLC-MS) identified around 480 differentially expressed metabolites, with the majority being significantly associated with pigment synthesis.•Analysis of clusters and pathways underscored the significance of pathways such as plant secondary metabolite biosynthesis, phenylpropanoid biosynthesis and plant hormone signal transduction in pigment synthesis. This study conducted a combined transcriptomics and metabolomics analysis in premature and mature developmental stages of Gardenia jasminoides Ellis fruits to identify the molecular mechanisms of pigment synthesis. The transcriptomics data produced high-quality clean data amounting to 46.98 gigabytes, exhibiting a mapping ratio of 86.36% to 91.43%. Transcriptomics analysis successfully identified about 3,914 differentially expressed genes which are associated with pivotal biological processes, including photosynthesis, chlorophyll, biosynthetic processes, and protein-chromophore linkage pathways. Functional diversity was clarified by the Clusters of Orthologous Groups (COG) classification, which focused mainly on pigment synthesis functions. Pathways analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) revealed critical pathways affecting pigment development. Metabolomics studies were carried out utilizing Ultra Performance Liquid Chromatography and mass spectrometry (UPLC-MS). About 480 metabolites were detected via metabolomics investigation, the majority of that were significantly involved in pigment synthesis. Cluster and pathway analyses revealed the importance of pathways such as plant secondary metabolite biosynthesis, biosynthesis of phenylpropanoids and plant hormone signal transduction in pigment synthesis. Current research advances our comprehension of the underlying mechanisms at the molecular level governing pigment synthesis in gardenia fruits, furnishing valuable insights for subsequent investigation