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SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis

Qun-Jie Zhang, Wei Li, Kui Li, Hong Nan, Cong Shi, Yun Zhang, Zhang-Yan Dai, Yang-Lei Lin, Xiao-Lan Yang, Yan Tong, Dan Zhang, Cui Lu, Chen-feng Wang, Xiao-xin Liu, Wen-Kai Jiang, Xing-Hua Wang, Xing-Cai Zhang, Zhong-Hua Liu, Evan E. Eichler, Li-Zhi Gao
doi: https://doi.org/10.1101/2020.01.02.892430
Qun-Jie Zhang
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Wei Li
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Kui Li
2Novogene Bioinformatics Institute, Building 301, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100083, China
3School of Life Sciences, Nanjing University, Nanjing 210023, China
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Hong Nan
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
5University of the Chinese Academy of Sciences, Beijing 100039, China
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Cong Shi
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
5University of the Chinese Academy of Sciences, Beijing 100039, China
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Yun Zhang
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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Zhang-Yan Dai
6Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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Yang-Lei Lin
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
5University of the Chinese Academy of Sciences, Beijing 100039, China
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Xiao-Lan Yang
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
5University of the Chinese Academy of Sciences, Beijing 100039, China
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Yan Tong
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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Dan Zhang
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Cui Lu
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Chen-feng Wang
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Xiao-xin Liu
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
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Wen-Kai Jiang
2Novogene Bioinformatics Institute, Building 301, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100083, China
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Xing-Hua Wang
7Yunnan Pu’er Tea Tree Breeding Station, No. 212, Zhenxing Avenue, Simao District, Pu Er 665099, Yunnan, China
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Xing-Cai Zhang
8John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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Zhong-Hua Liu
9Hunan Agricultural University, Changsha 410128, China
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Evan E. Eichler
10Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Li-Zhi Gao
1Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
4Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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  • For correspondence: Lgaogenomics@163.com
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Abstract

Tea is the oldest and most popular nonalcoholic beverage consumed in the world. It provides abundant secondary metabolites that account for its diverse flavors and health benefits. Here we present the first high-quality chromosome-length reference genome of C. sinensis var. sinensis using long read single-molecule real time (SMRT) sequencing and Hi-C technologies to anchor the ∼2.85-Gb genome assembly into 15 pseudo-chromosomes with a scaffold N50 length of ∼195.68 Mb. We annotated at least 2.17 Gb (∼74.13%) of repetitive sequences and high-confidence prediction of 40,812 protein-coding genes in the ∼2.92-Gb genome assembly. This accurately assembled genome allows us to comprehensively annotate functionally important gene families such as those involved in the biosynthesis of catechins, theanine and caffeine. The contiguous genome assembly provides the first view of the repetitive landscape allowing us to accurately characterize retrotransposon diversity. The large tea tree genome is dominated by a handful of Ty3-gypsy long terminal repeat (LTR) retrotransposon families that recently expanded to high copy numbers. We uncover the latest bursts of numerous non-autonomous LTR retrotransposons that may interfere with the propagation of autonomous retroelements. This reference genome sequence will largely facilitate the improvement of agronomically important traits relevant to the tea quality and production.

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Posted January 02, 2020.
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SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis
Qun-Jie Zhang, Wei Li, Kui Li, Hong Nan, Cong Shi, Yun Zhang, Zhang-Yan Dai, Yang-Lei Lin, Xiao-Lan Yang, Yan Tong, Dan Zhang, Cui Lu, Chen-feng Wang, Xiao-xin Liu, Wen-Kai Jiang, Xing-Hua Wang, Xing-Cai Zhang, Zhong-Hua Liu, Evan E. Eichler, Li-Zhi Gao
bioRxiv 2020.01.02.892430; doi: https://doi.org/10.1101/2020.01.02.892430
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SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis
Qun-Jie Zhang, Wei Li, Kui Li, Hong Nan, Cong Shi, Yun Zhang, Zhang-Yan Dai, Yang-Lei Lin, Xiao-Lan Yang, Yan Tong, Dan Zhang, Cui Lu, Chen-feng Wang, Xiao-xin Liu, Wen-Kai Jiang, Xing-Hua Wang, Xing-Cai Zhang, Zhong-Hua Liu, Evan E. Eichler, Li-Zhi Gao
bioRxiv 2020.01.02.892430; doi: https://doi.org/10.1101/2020.01.02.892430

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