Exploring transposable element-mediated adaptive trait evolution using a large fungal pathogen genome panel
Transposable elements (TEs) are implicated in adaptation in several species, but identifying adaptive TE insertions is challenging due to difficulties in confidently calling TE insertions from short-read data and a lack of phenotypic information. Examples of TE-mediated adaptation in Zymoseptoria tritici exist, but the role of TEs in 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.Leveraging 2,229 genomes sampled across the globe, we explore the dynamics of TEs under positive selection and their involvement in adaptive trait variation. We find significant TE expansions associated with specific populations, with large numbers of population-specific TE loci rising to high frequencies. We assess candidate polymorphic TEs for signatures of selection to determine their importance in the global spread of Z. tritici.