Transposable elements (TEs) are implicated in adaptation in several species, however identifying adaptive TE insertions remains challenging, often due to difficulties in confidently calling TE insertions from short-read data and a lack of detailed phenotypic information.

Zymoseptoria triciti is a globally distributed fungal pathogen of wheat, causing significant crop damage. TEs have caused genome size expansions in populations derived following the pathogen's spread from the centre of origin. Whilst some well-described examples of TE-mediated adaptation in Z. tritici exist, the significance of TEs in facilitating the species' global spread remains unknown. Rapid adaptation to new environments and increases in TE activity present an opportunity to systematically investigate the importance of TEs as a source of adaptive variation.

We manually curated 331 TE families using a pangenome assembly for Z. tritici from a panel of 19 reference-quality genomes. Leveraging 2,229 genomes sampled across the globe, we systematically explore the dynamics of TEs under positive selection and their involvement in adaptive trait variation. 

We generated a high-confidence TE variant set by validating calls in benchmarking using validation from PacBio data. We find significant TE copy number expansions associated with specific populations, including large increases in LTR, DNA, and MITE activity in North American populations. In contrast to other organisms, pathogen population structure can be resolved using TE insertion polymorphisms. When assessing TE abundance, we find large numbers of population-specific TE loci at common frequencies, ranging from 91 in European isolates to 895 in Oceanian isolates. With comprehensive trait and climate data for our genome panel, we assess candidate polymorphic TEs for signatures of selection to determine their importance in the global spread of Z. tritici. Overall, this work sheds light on the host-TE dynamics leading to the emergence of adaptive traits, and the processes.