The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants.

Abstract 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.