16Understanding the complex information stored in a genome remains challenging 17 since multiple connected regulatory mechanisms act at various scales to determine 18 function. Increased comprehension of genome function at scales beyond contiguous 19 nucleotides will help understand genetic diseases, the emergence of pathogenesis, 20 and more broadly the genomics of adaptation. Here we report the analysis of DNA 21 methylation, histone modification, and DNA accessibility in the plant pathogenic 22 65 Plant invading microbes use effectors to suppress, avoid or mitigate the plant 66 immune system 9,10 . Plants in-turn use a variety of plasma-membrane bound and 67 cytoplasmic receptors to recognize invasion, through recognition of the effector or 68

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in arms races with their hosts. In many pathogens, genes mediating aggressiveness cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. We now show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. Highly variable genomic regions evolved by frequent segmental duplications mediated by erroneous homologous recombination, often utilizing transposons, leading to genetic material that is free to diverge. Intriguingly, the duplicated regions are enriched in active transposons that further contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen aggressiveness.

Effectors are secreted by plant pathogens to facilitate infection, often through deregulation of host immune responses. During host colonization, race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae secrete the effector protein Ave1 that triggers immunity in tomato genotypes that encode the Ve1 immune receptor. Homologs of V. dahliae Ave1 (VdAve1) are found in plants and in few plant pathogenic microbes, and are differentially recognized by Ve1.However, how VdAve1 is recognized by Ve1 remained unknown. Interestingly, C-terminally affinity-tagged versions of VdAve1 failed to activate Ve1-mediated immunity, suggesting that exposure of the C-terminus of VdAve1 is required for Ve1-mediated recognition. This was confirmed by subsequent analysis of C-terminal deletion mutants, and by domain swap experiments. Although required, only the C-terminus of VdAve1 is not sufficient to activate Ve1-mediated immunity. Intriguingly, a three-dimensional structural model of VdAve1 revealed that the N-and C-termini co-localize on a surface-exposed patch of the VdAve1 protein. Indeed, subsequent analyses of N-terminal deletion mutants confirmed that also the N-terminus of VdAve1 is required to activate Ve1-mediated immunity. Thus, we conclude that a surfaceexposed patch of the VdAve1 protein that is composed by co-localized N-and C-termini is recognized by the tomato immune receptor Ve1.

Allopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. This increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their quest for host immune response evasion. Allodiploidization likely caused the shift in host range of the fungal pathogen plant Verticillium longisporum, as V. longisporum mainly infects Brassicaceae plants in contrast to haploid Verticillium spp. In this study, we investigated the allodiploid genome structure of V. longisporum and its evolution in the hybridization aftermath. The nuclear genome of V. longisporum displays a mosaic structure, as numerous contigs consists of sections of both parental origins. V. longisporum encountered extensive genome rearrangements, whereas the contribution of gene conversion is negligible. Thus, the mosaic genome structure mainly resulted from genomic rearrangements between parental chromosome sets. Furthermore, a mosaic structure was also found in the mitochondrial genome, demonstrating its bi-parental inheritance. In conclusion, the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in the hybridization aftermath. Conceivably, novel combinations of DNA sequence of different parental origin facilitated genome stability after hybridization and consecutive niche adaptation of V. longisporum.