Transposable elements create distinct genomic niches for effector evolution amongMagnaporthe oryzaelineages

Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). InMagnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. Here, we focus on 16AVReffector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies across all majorM. oryzaelineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determinedAVRgain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. EachAVRwas integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversifyAVRloci. We used the large genomic dataset to recapitulate the evolution of the rice blastAVR1-CO39locus. Taken together, our work demonstrates how TE dynamics are an integral component ofM. oryzaeeffector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.