Chromosome-scale de novo genome assembly and comparative analysis of the tomato pathogen Septoria lycopersici reveal features associated with pathogenicity

Septoria leaf spot, caused by Septoria lycopersici , is an economically important fungal disease affecting tomato production worldwide. However, genomic resources for this pathogen are limited, which hinders detailed studies of its biology, diversity, and evolution. To address this gap, S. lycopersici was isolated from symptomatic tomato leaves in North Carolina, U.S.A., and confirmed by morphological characteristics, pathogenicity testing, and molecular markers. We report, for the first time, a chromosome-level genome assembly for the S. lycopersici isolate SLML, generated using PacBio long-read and Illumina short-read sequencing. Additionally, a second isolate (SL2) was sequenced using Illumina short-read sequencing to provide preliminary insight into intraspecific variation. The SLML assembly spans 29.4 Mb with a contig N50 of 2.3 Mb and includes 13 chromosomes and a mitochondrial genome. Comparative genomic analysis with related Septoria species identified a diverse set of virulence-associated genes, including 420 carbohydrate-active enzymes (CAZymes), 40 secondary-metabolite biosynthetic gene clusters (BGCs), and 835 predicted secreted proteins, of which 197 were classified as putative effectors. Gene-content-based lifestyle analysis identified features consistent with hemibiotrophic pathogenic fungi. This high-quality genome assembly provides a foundational resource for future studies on the pathogenic mechanisms, genomic evolution, and population biology of S. lycopersici , ultimately supporting improved understanding of Septoria leaf spot.