Multi-platform sequencing explores the transcriptomics of terpenoid biosynthesis in Melaleuca alternifolia

Abstract

Leaves of Melaleuca alternifolia are abundant in essential oils comprising terpenoids and volatile organic compounds, which play an important role in plant abiotic stress response. However, the molecular mechanisms underlying terpenoid biosynthesis in M. alternifolia remain poorly understood. To fill this knowledge gap, we profiled terpenoid content and composition across four distinct growth phases using gas chromatography-mass spectrometry (GC/MS). We also performed an integrated analysis of gene expression in leaf tissues through full-length transcriptome sequencing combined with high throughput RNA sequencing. We identified 46,313 transcripts, 99 % (45,848 transcripts) of which were annotated using existing databases. Our study also revealed 2,792 transcription factors (TFs) and 1,812 alternative splicing (AS) events. Through weighted gene co-expression network analysis (WGCNA), we clustered these identified genes into 11 co-expressed modules. Notably, two modules—designated as blue and brown—were significantly correlated with essential oil content. Homologous annotation with the Arabidopsis database revealed that genes within the blue module are largely involved in the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, suggesting its pivotal role in essential oil synthesis in M. alternifolia. Furthermore, elevated expression levels of VAMP72 and DGK1 in the brown module indicate their potential function as negative regulators of essential oil synthesis. Our findings unveil key differentially expressed genes (DEGs) and pathways that can be targeted to enhance essential oil production in M. alternifolia. The identified TFs may serve as potential candidates for genetic modification through genome editing technologies. This research provides valuable insights into the processes involved in essential oil biosynthesis and highlights key genes for functional characterization in M. alternifolia.

Keywords

• Melaleuca alternifolia
• Iso-seq
• RNA-seq
• WGCNA