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.
DOI:10.1101/2020.01.02.892430

Authors: 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

以下来自科学网 http://news.sciencenet.cn/sbhtmlnews/2020/1/352632.shtm

小叶茶染色体级别基因组图谱首次完成

本报讯 近日，在线发表了中美科学家联合研究团队的最新成果，该团队采用单分子实时测序（SMRT）和 Hi-C技术，在20多个代表性小叶茶品种中选用杂合度较低的小叶茶良种“碧云”，将组装获得的约2.85Gb 的基因组序列挂载到了15 条假染色体上，在国际上首次获得了达到染色体级别的茶树中国茶变种的参考基因组序列。

论文通讯作者高立志告诉《中国科学报》，通过与基于基因组二代测序技术发表的小叶茶舒茶早基因组草图比较基因组学分析表明，该研究获得的基因组图谱scaffold N50长度高达195.68 Mb，在组装准确性与完整性上都得到了极大的提升；解析获得了包括茶多酚、茶氨酸和咖啡因生物合成相关基因在内的40812个蛋白编码基因的准确序列，首次及时地为全世界茶学研究者提供了准确的茶树基因信息。

“染色体级别的茶树‘碧云’参考基因组图谱的获得，让我们第一次看到了茶树基因组大小变异的动态历史与成因的真实面目。”高立志表示，利用三代测序技术获得的“碧云”茶树参考基因组使我们追溯到，在过去100万年中迅速扩增导致了庞大的茶树基因组。

这张图谱的绘制，将进一步推进决定茶叶适制性、风味和品质以及茶树全球生态适应性遗传基础的认识；加速茶树功能基因组学研究、性状解析、优异新基因发掘以及旨在提高茶叶品质和适应性的茶树新品种培育，为茶叶深加工产业又快又好地发展提供科技支撑；也将促进茶树起源与驯化这一重大科学问题的回答并推动全球野生茶树种质资源的遗传保护。（韩天琪）

相关论文信息：https://doi.org/10.1101/2020.01.02.892430《中国科学报》 (2020-01-07 第3版 农业科技)

See also:https://scholar.google.com/citations?user=2vDraMoAAAAJ&hl=en

Polyphenol and Self-Assembly: Metal Polyphenol Nanonetwork for Drug Delivery and Pharmaceutical Applications by Dr. Tea (Xingcai Zhang) etc https://doi.org/10.4155/fdd-2019-0001

Effect of Fermentation and Plucking Standards on the Quality of Tea Juice,  by Dr.Yong-Quan Xu, Dr. Xingcai Zhang, and Dr. Jun-Feng Yin etc. https://doi.org/10.1155/2018/4312875

Antitumor Activity of Tea Polyphenol Epigallocatechin Gallate (EGCG) Nanocomplexes (New Epigallocatechin Gallate (EGCG) Nanocomplexes Co-Assembled with 3-Mercapto-1-Hexanol
and Lactoglobulin for Improvement of Antitumor Activity. J. Biomed. Nanotechnol. 13, 805–814 (2017) by Dr. Xingcai Zhang, and Dr. Qizhen Du etc https://doi.org/10.1166/jbn.2017.2400 http://wteao.org/antitumor-activity-of-tea-polyphenol-egcg/

Tea and Cancer Prevention. J. Cancer Res. Updates 4 (2), 65-73. by Dr. Xingcai Zhang.DOI: http://dx.doi.org/10.6000/1929-2279.2015.04.02.4

SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis by Dr. Xingcai Zhang, Dr. Lizhi Gao etc doi: https://doi.org/10.1101/2020.01.02.892430

The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Molecular Plant, 2017 Dr. Lizhi Gao etc DOI: 10.1016/j.molp.2017.04.002