Integrative Transcriptomic and Metabolomic Analysis Reveals Regulatory Networks and Metabolite Dynamics in Gastrodia elata Flower Development

Flower development, a vital phase in the plant life cycle, involves intricate physiological and morphogenetic processes driven by dynamic molecular and metabolic processes. However, the specific molecular mechanisms and metabolite accumulation patterns during Gastrodia elata flower development remain largely unknown. This study utilized Illumina’s next-generation sequencing to analyze the G. elata flower transcriptome across three critical developmental stages, capturing gene expression changes, particularly those related to transcription factors that regulate flower formation and metabolite accumulation. FPKM analysis showed significant transcriptomic changes during G. elata flower development, while targeted metabolomics identified key metabolites with stage-specific variations via widely targeted metabolic profiling. Here, integrative transcriptome and metabolome analyses were performed to investigate floral genes and compounds in G. elata flowers at three different developmental stages. The differentially expressed genes (DEGs) and significant changes in metabolites (SCMs) involved in key biological pathways were identified. This approach aimed to identify functional genes or pathways jointly enriched in metabolites, thereby defining pathways linked to crucial biological phenotypes. By mapping DEGs and SCMs to KEGG pathways, the comprehensive network was constructed, uncovering functional relationships between gene expression and metabolite accumulation. This study proposes dynamic models of transcriptomic and metabolite changes, revealing key regulatory networks that govern G. elata flower development and potential applications.