Comparative transcriptome database for Camellia sinensis reveals genes important for flavonoid synthesis in tea plants

Tea, as one of the most popular beverages in the world, possesses a plethora of secondary metabolites that are beneficial to human health. Tea plants (Camellia sinensis) exhibit rich genetic diversity, where different cultivars can vary significantly in terms of yield, adaptability, morphology, and composition of secondary metabolites. Many tea cultivars have been the subject of much research interest, which have led to the accumulation of publicly available RNA-seq data. As such, it has become possible to systematically summarize the characteristics of different cultivars at the transcriptomic level, identify valuable functional genes, and infer gene functions through co-expression analysis. Here, the transcriptomes of 9 cultivars of Camellia sinensis were assembled and combined with the coding sequences of 13 cultivars of Camellia sinensis to study the differences and similarities of gene expression and biological functions among cultivars. To give access to this data, we present TeaNekT (https://teanekt.sbs.ntu.edu.sg/), a web resource that provides user-friendly tools and interactive visualizations that facilitates the prediction of gene functions of various tea cultivars. We used TeaNekT to perform cross-cultivar comparison of co-expressed gene neighborhoods, clusters, and tissue-specific gene expression. We show that the members of the chalcone synthase (CHS) gene family, important for flavonoid synthesis, exhibit the highest expression variability, specific expression in leaves and buds, and significant modulation by methyl jasmonate (MeJA) treatment. By using comparative co-expression tools of TeaNekT, we identified multiple conserved genes involved in flavonoid biosynthesis among cultivars that have not been previously studied, warranting further research.