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A Chromosome-Level Genome Assembly of Coffea arabica L. var. ‘Kona Typica’

ORCID IDs

Lyu https://orcid.org/0000-0002-8783-0722

Song https://orcid.org/0000-0002-1171-0636

Yin https://orcid.org/0000-0001-7667-881X

Matsumoto https://orcid.org/0000-0001-6070-8834

Yu https://orcid.org/0000-0001-5393-5764

Document Type

Article

Date of this Version

2025

Citation

Scientific Data (2025) 12: 1314

doi: 10.1038/s41597-025-05658-6

Comments

United States government work. Public domain

Abstract

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.

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