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

• Published in: Industrial crops and products 2024-12, Vol.222, p.119992, Article 119992
• Main Authors: Rawal, Hukam C., Borchetia, Sangeeta, Rohilla, Megha, Mazumder, Abhishek, Gogoi, Madhurjya, Patel, Pradeep Kumar, Ilango, R.Victor J., Das, Buddhadeb, Mazumder, Anirban Basu, Bandyopadhyay, Tanoy, Kumar, P.Mohan, Soundararajan, S., Bera, Biswajit, Mahadani, Pradosh, Saha, Gargi, Mukherjee, Sudipta, Sabhapondit, Santanu, Barooah, Anoop Kumar, Sharma, Tilak Raj, Singh, Nagendra Kumar, Mondal, Tapan Kumar
• Format: Article
• Language: English
• Subjects: Assam type; Evolution; Origin
• ISSN: 0926-6690
• DOI: 10.1016/j.indcrop.2024.119992

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/). •First chromosome-level reference assembly of Assam type tea (C. assamica).•Resequencing analysis with 150 tea accessions across the world to shed light on the genome evolution of tea.•Annotation and diversity analysis to find genes associated with characteristic features of tea.•List of genes involved in positive selection for domestication related traits of tea.•An Indian tea pan-genome covering genetic diversity to report core and variable genes.