The high-quality chromosome-scale genome of ‘Longjing 43’, a representative tea plant cultivar in China, was obtained by using the self-developed third-generation sequencing assembly algorithm to solve the complex genome assembly problem of tea plant genome with high heterozygosity and high repeat sequence ratio. Based on the in-depth resequencing of 139 tea accessions from around the world, the origin of cultivated tea plants from the perspective of population genetics is revealed for the first time, and the diferences in the selection pressure of genes related to flavor metabolism and disease resistance during the domestication of the two main varieties (C. sinensis var. sinensis and C. sinensis var. assamica) are found. The research results lay a solid theoretical foundation for the molecular breeding and evolution of the tea plant.

Characterization and quality of the LJ43 genome