| A Near Telomere-To-Telomere Genome Assembly of Coffea arabica (Mundo Novo) Provides Insights Into Its Secondary Metabolism | |
Liu, Yi1; Zong, Hang; Xing, Yaowu2 ; Jiao, Xi1; Liu, Zhuoya1; Niu, Yusheng; Yang, Zhiling2; Liu, Shimeng1; Wang, Yongqiang3; Zhao, Haodong4; Chen, Xianqing1; Li, Zhenzhu1; Wang, Xiao1; Cai, Jing; Wang, Wen; Wang, Zhongkai1
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| 2025 | |
| Source Publication | MOLECULAR ECOLOGY RESOURCES
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| ISSN | 1755-098X |
| Pages | - |
| Abstract | Arabica coffee (Coffea arabica) dominates global coffee production, accounting for over 60% of the world's coffee trade. The Mundo Novo cultivar, predominantly grown in Yunnan, China, represents a significant germplasm resource. However, the absence of a high-quality reference genome has hindered comprehensive genetic research and in-depth investigation of secondary metabolic pathways in Arabica. In this study, we present the first near telomere-to-telomere (T2T) genome assembly of Arabica, achieved through the integration of PacBio HiFi, Oxford Nanopore ultra-long, and Hi-C sequencing technologies, representing the highest-quality Arabica genome to date. Phylogenetic analysis of N-methyltransferases (NMTs), the key enzymes responsible for caffeine biosynthesis, revealed their independent evolution across caffeine-producing clades including coffee, cacao, and tea. Furthermore, GO enrichment analysis of expanded gene families at the Arabica ancestral node, combined with fruit-specific transcriptomic profiling, revealed that glycosyltransferases likely play a critical role in the secondary metabolism of Arabica. Notably, functional characterisation demonstrated that a UGT (uridine diphosphate glycosyltransferase, UGT) from the UGT29 subfamily, which exhibited increased gene copy number in the Arabica subgenome C than its ancestor, can directly convert Rebaudioside A (Reb A) into Rebaudioside M (Reb M) through a single-step enzymatic glycosylation. This direct pathway represents a crucial advancement over conventional multi-UGTs biosynthetic routes of Reb M, which is a highly desirable sweetener whereas with limited natural abundance. Taken together, this study not only provides a valuable genomic resource for studying the unique secondary metabolic processes in C. arabica but also accelerates innovative research frontiers for the synthetic biological production of the valuable sweetener Reb M. |
| Keyword | Arabica coffee NMTs Reb M secondary metabolism T2T genome assembly UGTs |
| Subject Area | Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology |
| DOI | 10.1111/1755-0998.70053 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:001581753000001 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/15662 |
| Collection | 2012年后新成立研究组 |
| Affiliation | 1.Northwestern Polytech Univ, Sch Ecol & Environm, Shaanxi Key Lab Qinling Ecol Intelligent Monitorin, Xian, Shaanxi, Peoples R China 2.Jiaxing Synbiolab Biotechnol Co Ltd, Jiaxing, Peoples R China 3.Chinese Acad Sci, Key Lab Trop Forest Ecol, Xishuangbanna Trop Bot Garden, Mengla, Peoples R China 4.Sanjie Inst Forage, Yangling, Peoples R China 5.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, State Key Lab Engn Biol Low Carbon Mfg, Tianjin, Peoples R China |
| Recommended Citation GB/T 7714 | Liu, Yi,Zong, Hang,Xing, Yaowu,et al. A Near Telomere-To-Telomere Genome Assembly of Coffea arabica (Mundo Novo) Provides Insights Into Its Secondary Metabolism[J]. MOLECULAR ECOLOGY RESOURCES,2025:-. |
| APA | Liu, Yi.,Zong, Hang.,Xing, Yaowu.,Jiao, Xi.,Liu, Zhuoya.,...&Wang, Zhongkai.(2025).A Near Telomere-To-Telomere Genome Assembly of Coffea arabica (Mundo Novo) Provides Insights Into Its Secondary Metabolism.MOLECULAR ECOLOGY RESOURCES,-. |
| MLA | Liu, Yi,et al."A Near Telomere-To-Telomere Genome Assembly of Coffea arabica (Mundo Novo) Provides Insights Into Its Secondary Metabolism".MOLECULAR ECOLOGY RESOURCES (2025):-. |
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| A Near Telomere-To-T（4590KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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