Evolutionary genomics of structural variation in the tea plant, Camellia sinensis

Structural variants (SVs) are a type of genetic variation that contribute substantially to phenotypic diversity and evolution. Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research. However, SVs have not been thoroughly discovered in the tea plant genomes. Herein, we constructed a large-scale SV map across a population of 107 resequenced genomes, including both ancient and cultivated tea plants. A total of 44,240 high-confident SVs were identified, including 34,124 DEL (deletions), 4,448 DUP (duplications), 2,503 INV (inversions), 544 INS (insertions) and 2,621 TRA (translocations). In total, 12,400 protein-coding genes were overlapped with SVs, of which 49.5% were expressed in all five tea tissues. SV-based analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results. We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids, biosynthesis of monoterpenoid, phenylpropanoid, fatty acid, and isoflavonoid, contributing to traits of agronomic interest in tea plants. In addition, a total of 27 terpene synthase (TPS) family genes were selected during domestication. These results indicate that these SVs could provide extensive genomic information for tea quality improvement.