First telomere-to-telomere gapless genome assembly of the blackleg fungus Plenodomus lingam

Blackleg disease, caused by the ascomycete fungus Plenodomus lingam (syn.: Leptosphaeria maculans), is the most devastating disease of oilseed rape worldwide. As a model organism for studying plant-fungus interactions, P. lingam has been extensively studied, yet telomere-to-telomere (T2T) genome assemblies have been lacking. Here, we report a high-quality T2T gapless genome assembly of P. lingam ‘brassicae’ strain 479-2, generated using MGI short reads, PacBio/Nanopore long reads, and Hi-C data. The assembly comprises 19 nuclear chromosomes totaling 40.74 Mb, each capped by telomeric repeats (CCCTAA/TTAGGG), and a complete circular mitochondrial genome of 169,227 bp. Key quality metrics include: 46.08% GC content, 30.09% repeat content, 98.5% complete BUSCOs (fungi_odb10), a consensus quality score of 45.86, and a low error rate of 2.59 × 10−5. Functional annotation predicted 9,818 protein-coding genes, including 807 cytochrome P450s, 464 carbohydrate-active enzymes, 808 secreted proteins, and 287 candidate effectors. This T2T assembly provides a gold-standard genomic resource for studies of pathogenicity, effector evolution, and host adaptation in P. lingam, and will advance research on plant-pathogen co-evolution.