Glandular trichomes (GTs) are epidermal outgrowths in which diverse specialized metabolites are synthesized and stored. The GT bearing species cannabis (Cannabis sativa L.) and its close relative hop (Humulus lupulus L.) have great pharmaceutical and industrial significance due to the specialized metabolites they produce, which differ between species. Gene regulatory network (GRN) analyses that compare organs and tissues within and across species are a powerful tool to identify genes that have major roles in organ functions. To understand the transcriptional programmes underlying GT-related processes, we generated transcriptome atlases of trichome, flower, leaf, stem, and root from cannabis, hop and tomato. We determined that on average 15.2%, 6.7% and 19.6% of the predicted cannabis, hop and tomato genes were expressed organ specifically, respectively. Transcription factors accounted for 7.0% (hop), 9.1% (cannabis) and 9.3% (tomato) of the organ/tissue-specific transcriptome and likely regulate organ/tissue-specific functions. Organ-specific expression was species-specific for some genes, whilst it was shared across species for others, and the number of shared organ/tissue-specific genes reflected phylogenetic distances between the species. We constructed GT GRNs specific to cannabis or hop, as well as GT GRNs predicted to be shared between species. Most of the genes in species-specific GRNs were associated with specialized metabolism pathways, consistent with the species-specific nature of specialized metabolism. Contrastingly, components of the GRNs shared between species were involved in highly conserved processes such as flavonoid biosynthesis, solute transport and the storage of metabolites. These transcriptome atlases are valuable resources to improve our knowledge of the extent of conservation of organ-specific genome regulation between species.
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