Exploring the developmental mechanisms of tea plant trichomes using genomics and single-cell transcriptome sequencing

Fuding Dahaocha, a triploid white tea cultivar widely cultivated in south China, exhibits distinctive traits including dense leaf trichomes, early sprouting, and robust stress resistance. Here, we present the first high-quality chromosome-level genome assembly of this triploid variety, resolved through integrated PacBio long-read sequencing and Hi-C scaffolding. The genome assembly spans 45 chromosomes with a scaffold N50 value of 182 Mbp. A total of 149 455 gene models were annotated and mapped to chromosomes, among which 30 568 were identified as protein-coding genes. The genome features high repetitiveness (65.9% transposable elements), heterozygosity, and three distinct haplotype sets with substantial allelic variation (17 601 triallelic genes), with the retained haplotype-specific genes potentially contributing to regulatory complexity through dosage effects. Genome completeness assessment revealed a BUSCO completeness of 99.0% (2303 out of 2326 conserved core genes identified), which included 40 single-copy (1.7%) and 2263 duplicated (97.3%) genes. Evolutionary analyses indicated conserved relationships among the three homologous chromosome sets. We also performed single-nucleus RNA sequencing on a sufficiently large pooled sample of leaf tissues to study trichome development, overcoming technical limitations posed by secondary metabolites and low protoplast isolation efficiency. This yielded a single-cell atlas for woody plants, identifying 35 trichome-specific marker genes and modeling developmental trajectories during epidermal differentiation. Functional validation identified CsCUT1 as a suppressor of trichome branching and CsMYB4 as a negative regulator of trichome initiation. Cell cycle analysis showed G2-phase dominance in developing trichomes. These findings provide a genetic framework for trichome development and offer resources for tea breeding.