A chromosome-level genome assembly of Coffea arabica L. var. ‘Kona Typica’
- Haomin Lyu
- Jinjin Song
- Yanbin Yin
- Ming-Li Wang
- Tracie Matsumoto
- Vaishnavi Annabhemoju
- Lyndel W. Meinhardt
- Sunchung Park
- Seunghyun Lim
- Dapeng Zhang
- Qingyi Yu
2025-07-29
Coffea arabica L. var. ‘Kona Typica’ is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of ‘Kona Typica’ using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, 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 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of ‘Kona Typica’ provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.