A chromosome-level genome assembly of Coffea arabica L. var. ‘Kona Typica’

Authors: LYU, HAOMIN - Hawaii Agricultural Research Center; SONG, JINJIN - Oak Ridge Institute For Science And Education (ORISE); YIN, YANBIN - University Of Nebraska; WANG, MING-LI - Hawaii Agricultural Research Center; Matsumoto Brower, Tracie; ANNABHEMOJU, VAISHNAVI - University Of Nebraska; Meinhardt, Lyndel; Park, Sunchung; LIM, SEUNGHYUM - Oak Ridge Institute For Science And Education (ORISE); Zhang, Dapeng; Yu, Qingyi

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/18/2025
Publication Date: 7/29/2025
Citation: Lyu, H., Song, J., Yin, Y., Wang, M., Matsumoto Brower, T.K., Annabhemoju, V., Meinhardt, L.W., Park, S., Lim, S., Zhang, D., Yu, Q. 2025. A chromosome-level genome assembly of Coffea arabica L. var. ‘Kona Typica’. Scientific Data. 12. Article 1314. https://doi.org/10.1038/s41597-025-05658-6.
DOI: https://doi.org/10.1038/s41597-025-05658-6

Interpretive Summary: Coffee is one of the most widely cultivated beverage crops in tropical and subtropical regions, renowned for its economic importance and cultural significance. Arabica coffee accounts for 60-70% of world production and is known for its smooth, well-balanced taste and lower caffeine content compared to Robusta coffee. ‘Kona Typica’ is renowned for its exceptional quality and flavor, and is the predominant variety in the Kona region. Despite its superior taste and quality, ‘Kona Typica’ is highly susceptible to pests and diseases. In this study, we present a chromosome-level genome assembly of ‘Kona Typica’ coffee constructed using PacBio long-read sequencing and Omni-C data. The resulting genome comprises 22 chromosomes with a total size of 1.13 Gbp and a scaffold N50 of 50.50 Mb. This high-quality 'Kona Typica' genome assembly provides a valuable resource for coffee research and improvement, enabling investigations into coffee genome evolution and genetic mapping of important traits, and facilitating the development of improved coffee cultivars with enhanced disease resistance and quality traits.

Technical Abstract: Coffea arabica L. var. ‘Typica’ is widely cultivated variety prized for its high cup quality, but its susceptibility to pests and diseases poses a significant threat to production and economic stability. A comprehensive understanding of its genome is crucial for developing disease-resistant and high-quality cultivars. In this study, we present a chromosome-scale genome assembly of Coffea arabica L. var. ‘Kona Typica’ generated using PacBio HiFi reads and Hi-C scaffolding technology. The final assembly spans 1.13Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified transposable elements comprising 65.16% of the genome. Comparative analysis with the ‘ET-39’ arabica genome identified the structural variations and revealed 524 genomic duplication and 17.27 Mb of genomic regions that were unique in the ‘Kona Typica’ genome, potentially associated with phenotypic variations. This high-quality 'Kona Typica' genome assembly provides a valuable resource for coffee research and improvement, enabling investigations into coffee genome evolution and genetic mapping of important traits, and facilitating the development of improved coffee cultivars with enhanced disease resistance and quality traits.