Insights into glandular trichome biology from analysis of organ‐specific gene expression programmes in cannabis, hop and tomato

Glandular trichomes (GTs) are epidermal outgrowths in which diverse specialised (secondary) metabolites are synthesised and stored. Cannabis (Cannabis sativa L.) and its close relative hop (Humulus lupulus L.) have pharmaceutical and industrial significance due to the presence of these metabolites in their GTs. We examined the conservation or divergence of the specific transcriptional programmes underlying GT biology. To achieve this, we generated transcriptome atlases of trichomes, flower, leaf, stem and root for cannabis, hop and tomato. We found that 12.9, 10.1 and 16.8% of cannabis, hop and tomato genes, respectively, were expressed organ/tissue specifically across all organs/tissues. Transcription factors (TFs) on average accounted for 7.5% of the organ-specific transcriptome and likely regulate organ-specific functions. We also conducted weighted gene co-expression network analysis and gene regulatory network (GRN) analysis to identify key regulators of GT function across the species and validated our predictions by DNA affinity purification sequencing for a subset of the cannabis and tomato GT TFs. The GRNs specific to cannabis or hop GTs were enriched for TFs and target genes associated with specialised metabolism, reflecting their species-specific nature. Conversely, the shared GRN components (identified via orthology analysis) were involved in highly conserved processes, such as flavonoid biosynthesis, solute transport and metabolite storage. Together, these GRNs and the associated transcriptome atlases are valuable resources to improve our knowledge of GT function and organ-specific genome regulation.