10.60507/FK2/G2TRGZVieira Salgado de Oliveira, Julie AnneJulie AnneVieira Salgado de Oliveira0000-0001-9930-6373University of BonnBöhnert, TimTimBöhnert0000-0003-1415-7896University of BonnPucker, BoasBoasPucker0000-0002-3321-7471University of Bonnbonndata2026Agricultural SciencesPucker, BoasUniversity of Bonn2026-09-032026-09-1811523173694719161408268886377389997478115265716972391606200289489288499640075365application/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gzipapplication/gziptext/plain1.0CC BY 4.0Here we present high-quality genome sequences and corresponding annotations of Muscari commutatum, a perennial herb in the Asparagaceae family. The study uncovers the flavonoid biosynthesis gene repertoire underlying anthocyanin pigmentation in this species. Using ONT long-read sequencing data, highly continuous genome assemblies were generated for both an anthocyanin-pigmented and an unpigmented M. commutatum plant. This data publication contains the genome sequences with corresponding annotations.German Network for Bioinformatics Infrastructure (de.NBI) and ELIXIR-DEForschungszentrum Jülich and W-de.NBI-001