Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

Author:

Zhang XingtanORCID,Chen Shuai,Shi Longqing,Gong Daping,Zhang Shengcheng,Zhao Qian,Zhan Dongliang,Vasseur LietteORCID,Wang Yibin,Yu Jiaxin,Liao Zhenyang,Xu Xindan,Qi Rui,Wang Wenling,Ma Yunran,Wang Pengjie,Ye NaixingORCID,Ma Dongna,Shi Yan,Wang Haifeng,Ma Xiaokai,Kong Xiangrui,Lin Jing,Wei Liufeng,Ma Yaying,Li Ruoyu,Hu Guiping,He Haifang,Zhang Lin,Ming RayORCID,Wang GangORCID,Tang HaibaoORCID,You MinshengORCID

Abstract

AbstractTea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.

Funder

National Natural Science Foundation of China

Fujian Province “2011 Collaborative Innovation Center”, the Chinese Oolong Tea Industry Innovation Center special project

The National Key R & D Program of China

Publisher

Springer Science and Business Media LLC

Subject

Genetics

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