Chromosome-level genome assembly of Fusarium tricinctum, a fungal pathogen associated with root rot in alfalfa.

Fusarium tricinctum is a globally devastating fungal pathogen associated with root rot disease in alfalfa. The absence of a complete genome sequence has hindered molecular investigations into its pathogenic mechanisms. This study reports the first chromosome-level genome assembly of the virulent F. tricinctum strain MsR-QD66, generated using a combined sequencing strategy integrating Illumina, PacBio HiFi, and Hi-C technologies. The 46.2 Mb assembly (scaffold N50 = 5.1 Mb) comprises 10 chromosomes with Merqury-validated abase accuracy (QV = 34.8, error rate <0.01%). The genome achieved 95.6% completeness according to CEGMA and complete BUSCO scores. This assembly comprises 13,594 protein-coding genes, 336 non-coding RNAs, and a comprehensive repertoire of repetitive elements. Functional annotation identified 1,871 transcription factors and 1,241 secreted proteins. Comparative genomics and virulence factor analyses revealed 527 genes linked to 36 key diseases across diverse hosts. This chromosome-level genome assembly provides a valuable resource for studying molecular mechanisms of F. tricinctum pathogenicity to alfalfa and will facilitate the development of sustainable strategies for managing root rot in alfalfa.