The poplar pathogen Sphaerulina musiva has a dynamic genome architecture marked by chromosomal inversions and changes in transposable element abundance

Fungal plant pathogens possess dynamic genomes, frequently shaped by transposable elements, that enable rapid adaptation to adverse conditions and host resistance mechanisms. However, assessing the adaptive significance of these genomic features remains challenging, in part due to the lack of high-quality genome assemblies for multiple members of a given species. To gain insights into genomic factors shaping pathogen evolution, we sequenced and assembled near-chromosome-scale genomes of 18 geographically diverse North American isolates of Sphaerulina musiva , a significant, important pathogen causing Septoria leaf spot and stem canker disease of poplar trees. Comparative genomic analyses indicated that all isolates possess 13 chromosomes with no evidence of accessory chromosomes. Transposable element (TE) content varied considerably among isolates (6.8 %–15.7 %), with a higher abundance in isolates from Oregon, British Columbia and Alberta, geographic regions outside the native range of S. musiva . The variation in TE content largely explained differences in genome size among isolates and suggested lineage-specific proliferation of TEs. Although a gene-based pangenome analysis indicated a relatively low percentage (9.5%) of accessory genes, this subset was enriched for candidate effectors. Our results indicate that S. musiva exhibits features of a ‘one-speed genome’ model. However, increased TE content is correlated with longer intergenic regions of candidate effector genes, suggesting that proliferation of TEs may be driving increased compartmentalization. Finally, synteny analysis revealed a total of 43 long chromosomal inversions with an average size of 293 kb that covered 34% of the S. musiva genome. These chromosomal inversions were more frequently observed in isolates from the pathogen’s native range in the Eastern USA, and at least one inversion was predicted to affect the organization of a secondary metabolite gene cluster. These findings provide novel insights into the genome structure, TE dynamics and chromosomal rearrangements of the poplar pathogen S. musiva , offering a foundation for understanding its evolution and adaptation across diverse geographic regions and host species.