Trichomes are the attractive cells for terpenoids biosynthesis and accumulation in Artemisia annua. However, the molecular process underlying the trichome of A. annua is not yet fully elucidated. In this study, we performed joint analysis on multi-tissue transcriptome data to investigate trichome-specific expression patterns. A total of 6646 genes were screened and highly expressed in trichome, including artemisinin biosynthetic genes, such as ADS and CYP71AV1. Mapman and KEGG pathway enrichment analysis showed that trichome-specific genes were mainly enriched in lipid metabolism and terpenoids metabolism. These trichome-specific genes were analyzed by a weighted gene co-expression network analysis (WGCNA) and the blue module linked to terpenoid backbone biosynthesis was determined. Hub genes correlated with the artemisinin biosynthetic genes were selected based on TOM value. ORA, BAMT, AATL1, ULP1 and TUB were revealed as key hub genes for regulating artemisinin biosynthesis. In summary, the identified trichome-specific genes, modules, pathways and hub genes provide clues and shed light on the potential regulatory mechanisms of artemisinin biosynthesis in trichomes in A. annua.
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