Implications of the Three-dimensional Chromatin Organization for Genome Evolution in a Fungal Plant Pathogen

Overview

Journal Nat Commun

Specialty Biology

Date 2024 Feb 24

PMID 38402218

Authors

David E Torres

H Martin Kramer

Vittorio Tracanna

Gabriel L Fiorin

David E Cook

Michael F Seidl

Bart P H J Thomma

Affiliations

Soon will be listed here.

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.

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