{"title":"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","authors":"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","doi":"10.1016/j.indcrop.2024.119992","DOIUrl":null,"url":null,"abstract":"<div><div>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 (<em>Camellia assamica</em>) and China (<em>C. sinensis</em> var. <em>assamica</em>). Single copy gene-based study has confirmed divergence of TV 1 from China type tea (<em>C. sinensis</em> var. <em>sinensis</em>) 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; <span><span>https://indianteagenome.in/</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":13581,"journal":{"name":"Industrial Crops and Products","volume":"222 ","pages":"Article 119992"},"PeriodicalIF":5.6000,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"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\",\"authors\":\"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\",\"doi\":\"10.1016/j.indcrop.2024.119992\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>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 (<em>Camellia assamica</em>) and China (<em>C. sinensis</em> var. <em>assamica</em>). Single copy gene-based study has confirmed divergence of TV 1 from China type tea (<em>C. sinensis</em> var. <em>sinensis</em>) 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; <span><span>https://indianteagenome.in/</span><svg><path></path></svg></span>).</div></div>\",\"PeriodicalId\":13581,\"journal\":{\"name\":\"Industrial Crops and Products\",\"volume\":\"222 \",\"pages\":\"Article 119992\"},\"PeriodicalIF\":5.6000,\"publicationDate\":\"2024-11-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Industrial Crops and Products\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0926669024019691\",\"RegionNum\":1,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURAL ENGINEERING\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Industrial Crops and Products","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0926669024019691","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURAL ENGINEERING","Score":null,"Total":0}
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
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/).
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.
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