The population genetics of adaptation through copy number variation in a fungal plant pathogen

<jats:title>Abstract</jats:title><jats:p>Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, <jats:italic>Rhynchosporium commune</jats:italic>, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell‐wall‐degrading enzymes). We perform genome‐wide association studies (GWAS) and identify a large segmental duplication of <jats:italic>CYP51A</jats:italic> that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome‐wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV‐focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.</jats:p>