Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

Weiyi Zhang,Björn Usadel,Yafei Guo,Dejiang Ni,Fei Guo,Pu Wang,Federico Scossa,Wei Chen,Alisdair R Fernie,Hu Wan ,Anting Zhu,Haiji Qiu,Saleh Alseekh,Youjun Zhang,Xinxin Jia,Maximilian Schmidt ,Qinghua Zhang,Xiaoliang Zhang,Daili Li,Li Xu,Weiwei Wen

doi:10.1038/s41467-020-17498-6

Abstract

Wild teas are valuable genetic resources for studying domestication and breeding. Here we report the assembly of a high-quality chromosome-scale reference genome for an ancient tea tree. The further RNA sequencing of 217 diverse tea accessions clarifies the pedigree of tea cultivars and reveals key contributors in the breeding of Chinese tea. Candidate genes associated with flavonoid biosynthesis are identified by genome-wide association study. Specifically, diverse allelic function of CsANR, CsF3’5’H and CsMYB5 is verified by transient overexpression and enzymatic assays, providing comprehensive insights into the biosynthesis of catechins, the most important bioactive compounds in tea plants. The inconspicuous differentiation between ancient trees and cultivars at both genetic and metabolic levels implies that tea may not have undergone long-term artificial directional selection in terms of flavor-related metabolites. These genomic resources provide evolutionary insight into tea plants and lay the foundation for better understanding the biosynthesis of beneficial natural compounds.

Highlights

Wild teas are valuable genetic resources for studying domestication and breeding
We demonstrate the utilization of the genome sequence and diverse natural populations of tea in the identification of genes and functional variations that regulate the content of catechins and gallic acid (GA) in tea leaves
There were 5453 Pacific Biosciences (PacBio) contigs linked by high-resolution chromosome conformation capture (Hi-C), yielding a genome size of 3.11 Gbp with 1237 scaffolds and an N50 of 204.21 Mb, and 99.55% of the entire genome sequences were anchored on 15 chromosomes (Table 1; Supplementary Method 1; Supplementary Tables 1–6; Supplementary Figs. 2–6). 87.41% of the genome was found to be repetitive, including a large proportion (76.59%) of long terminal repeat (LTR) transposable elements (Fig. 1; Supplementary Figs. 7, 8; Supplementary Tables 7–9)

Summary

Introduction

Wild teas are valuable genetic resources for studying domestication and breeding. Here we report the assembly of a high-quality chromosome-scale reference genome for an ancient tea tree. The inconspicuous differentiation between ancient trees and cultivars at both genetic and metabolic levels implies that tea may not have undergone long-term artificial directional selection in terms of flavor-related metabolites These genomic resources provide evolutionary insight into tea plants and lay the foundation for better understanding the biosynthesis of beneficial natural compounds. We demonstrate the utilization of the genome sequence and diverse natural populations of tea in the identification of genes and functional variations that regulate the content of catechins and gallic acid (GA) in tea leaves. These resources would facilitate the genetic improvement of tea plants as well as advance our understanding of the biosynthesis of healthbeneficial natural products in tea

Methods

Results

Conclusion