Metabolome and transcriptome revealed the biosynthesis pathway of aromatic compounds in <i>Ocimum basilicum</i> var. <i>pilosum</i>

The aromatic plant <italic>Ocimum basilicum</italic> var. <italic>pilosum</italic>, a Lamiaceae family member, is renowned for volatile organic compounds (VOCs), which have diverse applications in the culinary, medicinal, and aromatic industries. Despite its high economic and aromatic value, the biosynthetic pathway of VOCs is not well understood. This study employed metabolomic and transcriptomic approaches to explore the biosynthesis of VOCs in <italic>O. basilicum</italic> var. <italic>pilosum</italic>. Volatile metabolome analysis identified 151 compounds, with leaves serving as the primary source of VOCs. Phenylpropanes were identified as the major components, accounting for approximately 50% of the total VOC content in leaves, with methyl cinnamate and anethole being the predominant constituents. Illumina and PacBio sequencing identified 7,843 novel genes and 20,405 differentially expressed genes. Correlation analyses indicated that several transcription factors, including AP2/ERF-ERF, bHLH, and MYB families, are involved in the biosynthesis of methyl cinnamate and anethole. Additionally, the study identified 2,889 long non-coding RNAs and 10,427 instances of alternative splicing. Importantly, the biosynthetic pathways for methyl cinnamate and anethole were reconstructed. Two <italic>CBG</italic> genes (TCONS_00000475 and PB.4387.1) and two <italic>ACT</italic> genes (TCONS_00055847 and TCONS_00064938) were found to correlate with methyl cinnamate biosynthesis, whereas no gene expression showed a positive correlation with anethole content. This study elucidates the metabolic pathways and regulatory mechanisms underlying the biosynthesis of aromatic compounds in <italic>O. basilicum</italic> var. <italic>pilosum</italic>. The findings provide a foundation for enhancing the quality and yield of essential oils, offering valuable insights into the molecular breeding and cultivation strategies of aromatic plants.