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

Abstract

Camellia sinensis 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.

Acknowledgements

This work was supported by the National Key Research and Development Program of China during the 13th Five-Year Plan Period ‘Screening of Eco-Economical Tea Cultivars for Oolong Tea and White Tea with Supporting Cultivation Techniques’ (2019YFD01001601), the Major Science and Technology Special Project in Fujian Province (2024NZ029030), the Open Research Project of China White Tea Research Institute ‘Exploration, Conservation and Identification of Elite Tea Germplasm Resources in Fuding’ (BCY2021K01), and the Cooperative Research Project of Fuding Tea Industry Development Center ‘Construction of Chinese White Tea Germplasm Repository and Whole-Genome Sequencing of “Fuding Dahaocha” Tea Cultivar’ (KH220095A).

Author contributions

X.D., X.Z., and W.S. conceived and designed the experiments. X.D., Y.T., and Q.Z. performed the experiments. X.D., Y.T., Q.Z., W.K., X.L., X.C., and Z.C. analyzed the data. X.D., Y.T., and Q.Z. wrote the article. X.Z. and W.S. contributed to the writing review.

Data availability

The data that support the findings of this study are available in the supplementary material of this article. Genomic and single-cell sequencing data generated in this study have been deposited in the National Genomics Data Center under BioProject accession number CRA033556 and are publicly accessible.

Conflicts of interest statement:

The authors declare no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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