Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
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.
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dig-wur-nl-wurpubs-6278662024-12-04 Torres, David E. Kramer, H.M. Tracanna, Vittorio Fiorin, Gabriel L. Cook, David E. Seidl, Michael F. Thomma, Bart P.H.J. Article/Letter to editor Nature Communications 15 (2024) 1 ISSN: 2041-1723 Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen 2024 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. en application/pdf https://research.wur.nl/en/publications/implications-of-the-three-dimensional-chromatin-organization-for- 10.1038/s41467-024-45884-x https://edepot.wur.nl/652203 Life Science https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/ Wageningen University & Research |
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Life Science Life Science Torres, David E. Kramer, H.M. Tracanna, Vittorio Fiorin, Gabriel L. Cook, David E. Seidl, Michael F. Thomma, Bart P.H.J. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
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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. |
format |
Article/Letter to editor |
topic_facet |
Life Science |
author |
Torres, David E. Kramer, H.M. Tracanna, Vittorio Fiorin, Gabriel L. Cook, David E. Seidl, Michael F. Thomma, Bart P.H.J. |
author_facet |
Torres, David E. Kramer, H.M. Tracanna, Vittorio Fiorin, Gabriel L. Cook, David E. Seidl, Michael F. Thomma, Bart P.H.J. |
author_sort |
Torres, David E. |
title |
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
title_short |
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
title_full |
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
title_fullStr |
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
title_full_unstemmed |
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
title_sort |
implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen |
url |
https://research.wur.nl/en/publications/implications-of-the-three-dimensional-chromatin-organization-for- |
work_keys_str_mv |
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