Significance: A high-quality genome assembly of Camellia sinensis var. sinensis facilitates genomic, transcriptomic, and metabolomic analyses of the quality traits that make tea one of the world’s most-consumed beverages. The specific gene family members critical for biosynthesis of key tea metabolites, monomeric galloylated catechins and theanine, are indicated and found to have evolved specifically for these functions in the tea plant lineage. Two whole-genome duplications, critical to gene family evolution for these two metabolites, are identified and dated, but are shown to account for less amplification than subsequent paralogous duplications. These studies lay the foundation for future research to understand and utilize the genes that determine tea quality and its diversity within tea germplasm.

Phospholipase D (PLD) and protein phosphatase 2C (PP2C) both play a role in mediating plant responses to abscisic acid (ABA). In this article, we show that PLDα1 and its product, phosphatidic acid (PA), regulate a PP2C, ABI1, which is a negative regulator of ABA responses in Arabidopsis . Leaves from a T-DNA insertional mutant of PLD α 1 and PLD α 1 -antisense plants lose more water than do wild-type plants. The stomatal closure of PLD α 1 -null leaves is insensitive to ABA but is promoted by PA. ABA treatment promotes an increase in PA from phosphatidylcholine in wild type but not in PLD α 1 -null cells. PLDα1-derived PA binds to ABI1; the PA–ABI1 binding is demonstrated by coprecipitating PA with ABI1 from plant cells, measuring binding of PA from vesicles to ABI1, and assaying ABI1 bound to PA immobilized on a filter. Deletion and site-specific mutational analyses show that arginine 73 in ABI1 is essential for PA–ABI1 binding. PA binding decreases the phosphatase activity of ABI1. The lack of ABA-induced production of PA in PLD α 1 -null cells results in a decrease in the association of ABI1 with the plasma membrane in response to ABA. These results indicate that PA produced by PLDα1 inhibits the function of the negative regulator ABI1, thus promoting ABA signaling. The identification of ABI1 as a direct target of the lipid messenger PA provides a functional link between the two families of important signaling enzymes, PLD and PP2C.

Tea plant is an important economic crop, which produces the world's oldest and widely consumed tea beverages. We here present a high-quality reference genome of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes, 70.38% of which are LTR retrotransposons. We show the evidence that LTR-RTs play critical roles in the genome size expansion and transcriptional diversification of tea plant genes through preferential gene insertions in promoter regions and introns. Genes, particularly those for terpene biosynthesis, associated with tea aroma and stress resistance are significantly amplified forming gene clusters through recent tandem duplications in the tea plant genome. Phylogenetic analyses of the sequences of 81 tea plant accessions of diverse origins revealed three well-differentiated tea plant populations, supporting the proposition for the southwest origin of the cultivated tea plants in China and its later spreading to western Asian through introduction. Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome, particularly those associated with tea quality and stress resistance. The genomic sequences of the reported reference and resequenced tea plant accessions provided valuable resources for future functional genomic and breeding research of tea plants and understanding the genome evolution of flowering plants.