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Coffee, one of the most important economic crops worldwide, is widely cultivated in tropical and subtropical regions and serves as a major source of income for many countries and regions. Caffeine (1,3,7-trimethylxanthine) is the main metabolite in coffee beans and related products, which not only imparts the characteristic bitter taste and stimulates effect of coffee but also exerts multiple biological functions. The N-methyltransferase (NMT) gene family plays a key role in the caffeine biosynthetic pathway. Therefore, systematic identification of coffee NMT family members and analysis of the expression patterns at different developmental stages are of great importance for investigating caffeine metabolism, improving coffee quality, and breeding stress-resistant varieties. In this study, a total of 27 NMT genes were identified in allotetraploid Coffea arabica, including 14 genes from the C subgenome and 13 from the E subgenome, distributed across 10 chromosomes. Gene structure analysis revealed that family members shared similar motif compositions but differed in intron arrangement and number. Cis-acting element analysis showed that the promoters of C. arabica NMT genes were enriched with various regulatory elements related to light response, stress response and hormone signaling, and contained transcription factor binding sites such as MYB, MYC and W-box. Transcriptome analysis further demonstrated that NMT genes exhibited dynamic expression during fruit development, with the ripening stage showing the highest number of differentially expressed genes (14 703), while the expansion stage showed the lowest (4419). Moreover, C. arabica NMT genes displayed clear temporal and tissue-specific expression patterns. Weighted gene co-expression network analysis (WGCNA) identified 12 co-expression modules, among which the ivory, coral1 and darkolivegreen modules were enriched in pathways related to environmental stress and protein folding, energy metabolism and nucleic acid metabolism, respectively. Core gene network analysis revealed the critical roles of NMT genes in caffeine metabolism, stress response, and developmental regulation. Taken together, this study systematically identified the NMT gene family in allotetraploid C. arabica, characterized the expression patterns during different stages of fruit development, and elucidated the potential functional differentiation, thereby providing a theoretical basis for coffee breeding.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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