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

Xingtan Zhang; Shuai Chen; Longqing Shi; Daping Gong; Shengcheng Zhang; Qian Zhao; Dongliang Zhan; Liette Vasseur; Yibin Wang; Jiaxin Yu; Zhenyang Liao; Xindan Xu; Rui Qi; Wenling Wang; Yunran Ma; Pengjie Wang; Naixing Ye; Dongna Ma; Yan Shi; Haifeng Wang; Xiaokai Ma; Xiangrui Kong; Jing Lin; Liufeng Wei; Yaying Ma; Ruoyu Li; Guiping Hu; Haifang He; Lin Zhang; Ray Ming; Gang Wang; Haibao Tang; Minsheng You

doi:10.1038/s41588-021-00895-y

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

Xingtan Zhang, Shuai Chen, Longqing Shi, Daping Gong, Shengcheng Zhang, Qian Zhao, Dongliang Zhan, Liette Vasseur, Yibin Wang, Jiaxin Yu, Zhenyang Liao, Xindan Xu, Rui Qi, Wenling Wang, Yunran Ma, Pengjie Wang, Naixing Ye, Dongna Ma, Yan Shi, Haifeng WangXiaokai Ma, Xiangrui Kong, Jing Lin, Liufeng Wei, Yaying Ma, Ruoyu Li, Guiping Hu, Haifang He, Lin Zhang, Ray Ming, Gang Wang, Haibao Tang, Minsheng You

Plant Biology

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Abstract

Tea 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.

Original language	English (US)
Pages (from-to)	1250-1259
Number of pages	10
Journal	Nature Genetics
Volume	53
Issue number	8
Early online date	Jul 15 2021
DOIs	https://doi.org/10.1038/s41588-021-00895-y
State	Published - Aug 2021

ASJC Scopus subject areas

Genetics

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Zhang, X., Chen, S., Shi, L., Gong, D., Zhang, S., Zhao, Q., Zhan, D., Vasseur, L., Wang, Y., Yu, J., Liao, Z., Xu, X., Qi, R., Wang, W., Ma, Y., Wang, P., Ye, N., Ma, D., Shi, Y., ... You, M. (2021). Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nature Genetics, 53(8), 1250-1259. https://doi.org/10.1038/s41588-021-00895-y

Zhang, X, Chen, S, Shi, L, Gong, D, Zhang, S, Zhao, Q, Zhan, D, Vasseur, L, Wang, Y, Yu, J, Liao, Z, Xu, X, Qi, R, Wang, W, Ma, Y, Wang, P, Ye, N, Ma, D, Shi, Y, Wang, H, Ma, X, Kong, X, Lin, J, Wei, L, Ma, Y, Li, R, Hu, G, He, H, Zhang, L, Ming, R, Wang, G, Tang, H & You, M 2021, 'Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis', Nature Genetics, vol. 53, no. 8, pp. 1250-1259. https://doi.org/10.1038/s41588-021-00895-y

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abstract = "Tea 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.",

author = "Xingtan Zhang and Shuai Chen and Longqing Shi and Daping Gong and Shengcheng Zhang and Qian Zhao and Dongliang Zhan and Liette Vasseur and Yibin Wang and Jiaxin Yu and Zhenyang Liao and Xindan Xu and Rui Qi and Wenling Wang and Yunran Ma and Pengjie Wang and Naixing Ye and Dongna Ma and Yan Shi and Haifeng Wang and Xiaokai Ma and Xiangrui Kong and Jing Lin and Liufeng Wei and Yaying Ma and Ruoyu Li and Guiping Hu and Haifang He and Lin Zhang and Ray Ming and Gang Wang and Haibao Tang and Minsheng You",

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AU - Zhang, Shengcheng

AU - Zhao, Qian

AU - Zhan, Dongliang

AU - Vasseur, Liette

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AU - Yu, Jiaxin

AU - Liao, Zhenyang

AU - Xu, Xindan

AU - Qi, Rui

AU - Wang, Wenling

AU - Ma, Yunran

AU - Wang, Pengjie

AU - Ye, Naixing

AU - Ma, Dongna

AU - Shi, Yan

AU - Wang, Haifeng

AU - Ma, Xiaokai

AU - Kong, Xiangrui

AU - Lin, Jing

AU - Wei, Liufeng

AU - Ma, Yaying

AU - Li, Ruoyu

AU - Hu, Guiping

AU - He, Haifang

AU - Zhang, Lin

AU - Ming, Ray

AU - Wang, Gang

AU - Tang, Haibao

AU - You, Minsheng

PY - 2021/8

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N2 - Tea 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.

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

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