Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality

Abstract

SignificanceA 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.

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

“…The combined de novo and homology‐based methods were used to detect transposable elements (TEs) in the tea plant genome (Wei et al ., ). This identified a total amount of 1.86 Gb TE sequences that covers 64% of the nongapped tea plant genome assembly (Table ).…”

“…sinensis cv. shuchazao) is 3.14 Gb (2.89 Gb without N) that consists of 14 051 scaffolds and 94 321 contigs (Wei et al ., ) (Table ). The contig and scaffold N50 is 67.07 kb and 1.39 Mb, respectively.…”

“…The current tea plant genome assembly hosts a total of 33 932 high‐confidence genes (Wei et al ., ) (Table ). They are functionally annotated using different databases, including NR database (33 380; 98.37%), COG database (13 757; 40.54%), KOG database (19 230; 56.67%), PFAM database (27 262; 80.34%), GO database (15 138; 44.61%), KEGG database (27 267; 80.36%), InterPro database (27 262; 80.34%), TAIR database (32 122; 94.67%) and the best hits in C. sinensis var.…”

“…However, tea is the oldest and the world's most popular nonalcohol beverage with significant economic and medicinal importance; the lacking of reference genome basically hampers the urgent needs to utilize this precious genetic resource towards modern molecular breeding. To address this, we spend more than 10 years to generate a high‐quality reference genome of tea plant using two most advanced sequencing technologies, including PacBio long‐read and Illumina paired‐end sequencing (Wei et al ., ). Using the genomic, phylogenetic, transcriptomic and phytochemical approaches, we identified and functionally validated a key gene involving in the biosynthesis of theanine, an important characteristic compound associated with tea quality, and meanwhile showed strong evidences that the unique properties associated with tea cultivation and selection are the products of a series of dynamic genome evolutionary events.…”

“…Using the genomic, phylogenetic, transcriptomic and phytochemical approaches, we identified and functionally validated a key gene involving in the biosynthesis of theanine, an important characteristic compound associated with tea quality, and meanwhile showed strong evidences that the unique properties associated with tea cultivation and selection are the products of a series of dynamic genome evolutionary events. This broadens our understanding of the genetic basis of biosynthesis of the major characteristic secondary metabolites of tea plant that determines the tea quality and thus would promote the germplasm utilization for breeding new improved tea varieties (Wei et al ., ).…”