Single-nucleus RNA sequencing reveals the developmental trajectory and transcriptional regulatory networks of trichomes in Artemisia annua.

Sweet wormwood (Artemisia annua) produces and deposits artemisinin in its glandular trichomes but the molecular mechanisms of trichome development remain poorly understood. Here, we conduct single-nucleus RNA sequencing of 10-day-old A. annua seedlings, revealing the specific RNA expression of the leaf trichome cells. The reconstruction of the developmental trajectory of trichome cells not only identifies novel expressed genes, but also elucidates trichome development involved in photosynthesis, auxin biosynthesis, and cutin biosynthesis. By integrating the developmental trajectory of trichome cells with histochemical assays, we identified several genes not previously reported to be involved in trichome development, such as TOE3, MYB1, WRKY10, and ZNF. Moreover, we identified a gene in subcluster 0 encoding a previously unknown WD40 repeat nuclear protein, WDR1, potentially involved in trichome development. We showed that WDR1 not only interacts with the transcription factor SPL9 and enhances its ability to activate HD1 expression, but also directly binds to the transcription factor HD1 itself, thereby forming a regulatory feedback loop that modulates trichome development in A. annua. This study reveals a previously uncharacterized gene that regulates trichome development in A. annua based on single-cell transcriptome analysis. The results presented here offer unprecedented insight into a new pathway for enhancing trichome density and artemisinin production.