Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

David E. Torres, H. Martin Kramer, Vittorio Tracanna, Gabriel L. Fiorin, David E. Cook, Michael F. Seidl () and Bart P. H. J. Thomma ()
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David E. Torres: Wageningen University and Research
H. Martin Kramer: Wageningen University and Research
Vittorio Tracanna: University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS)
Gabriel L. Fiorin: Wageningen University and Research
David E. Cook: Wageningen University and Research
Michael F. Seidl: Wageningen University and Research
Bart P. H. J. Thomma: Wageningen University and Research

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

Date: 2024
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DOI: 10.1038/s41467-024-45884-x

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