First chromosome-scale genome of Indian tea (Camellia assamica Masters; syn C. sinensis var assamica) cultivar TV 1 reveals its evolution and domestication of caffeine synthesis

IF 5.6 1区农林科学 Q1 AGRICULTURAL ENGINEERING Industrial Crops and Products Pub Date : 2024-11-09 DOI:10.1016/j.indcrop.2024.119992

Hukam C. Rawal , Sangeeta Borchetia , Megha Rohilla , Abhishek Mazumder , Madhurjya Gogoi , Pradeep Kumar Patel , R.Victor J. Ilango , Buddhadeb Das , Anirban Basu Mazumder , Tanoy Bandyopadhyay , P.Mohan Kumar , S. Soundararajan , Biswajit Bera , Pradosh Mahadani , Gargi Saha , Sudipta Mukherjee , Santanu Sabhapondit , Anoop Kumar Barooah , Tilak Raj Sharma , Nagendra Kumar Singh , Tapan Kumar Mondal

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Abstract

Botanically, there are two main types of tea i.e. China and Assam type, predominant in China and India, respectively. Different chromosome-level assemblies of China type tea genomes have been reported recently but none for Assam type. Thus, in the present study, genome assembly of most popular Assam type Indian tea cultivar, TV 1 was decoded at chromosome-scale and analyzed to understand the domestication, variations, and evolutionary differences between China and Assam type teas. Whole genome duplication (WGD) study has confirmed close collinearity and recent WGD events between Assam type teas from India (Camellia assamica) and China (C. sinensis var. assamica). Single copy gene-based study has confirmed divergence of TV 1 from China type tea (C. sinensis var. sinensis) approximately 5.5 MYA, and SNP-based analysis of 150 genotypes across the world supports their independent domestication. Moreover, 512 genes in TV 1 were found positively selected during domestication events between caffeine and non-caffeine groups. At 93 fusion genes per species per million years rate, 400 fusion genes were found with no shared recent fusion events between China and Assam type tea. Secondary metabolite profiling has yielded several metabolic compounds such as caffeine, theophylline, and catechins. All these resources were documented in Tea India Genome e-Resource (TIGeR; https://indianteagenome.in/).

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印度茶（Camellia assamica Masters; syn C. sinensis var assamica）栽培品种 TV 1 的首个染色体级基因组揭示了其进化和咖啡因合成的驯化过程

在植物学上，有两种主要的茶叶类型，即中国型和阿萨姆型，分别在中国和印度占主导地位。最近有报道称，中国型茶叶基因组在染色体水平上进行了不同的组装，但阿萨姆型茶叶基因组组装尚无报道。因此，本研究对印度最受欢迎的阿萨姆型茶叶栽培品种 TV 1 的基因组进行了染色体解码和分析，以了解中国和阿萨姆型茶叶之间的驯化、变异和进化差异。全基因组复制（WGD）研究证实了印度阿萨姆型茶（Camellia assamica）和中国阿萨姆型茶（C. sinensis var.）基于单拷贝基因的研究证实了 TV 1 与中国茶叶（C. sinensis var.此外，TV 1 中的 512 个基因在咖啡因组和非咖啡因组之间的驯化过程中被正向选择。按照每百万年每个物种 93 个融合基因的速度计算，发现中国和阿萨姆型茶叶之间有 400 个融合基因，没有共同的近期融合事件。次生代谢物分析发现了多种代谢化合物，如咖啡因、茶碱和儿茶素。所有这些资源都记录在印度茶叶基因组电子资源（TIGeR; https://indianteagenome.in/）中。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Industrial Crops and Products 农林科学-农业工程

CiteScore

9.50

自引率

8.50%

发文量

1518

审稿时长

43 days

期刊介绍： Industrial Crops and Products is an International Journal publishing academic and industrial research on industrial (defined as non-food/non-feed) crops and products. Papers concern both crop-oriented and bio-based materials from crops-oriented research, and should be of interest to an international audience, hypothesis driven, and where comparisons are made statistics performed.