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Three-dimensional genome architecture of the pathogenic oomycete Phytophthora capsici provides insights into its chromatin architecture and regulatory complexity
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DOI：10.1038/s42003-026-10760-5.png)
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Abstract
En 中文
Chromosomes are folded hierarchically into compartments, domains, and chromatin loops within the three-dimensional (3D) nuclear space. Despite their relevance for agriculture, little is known about the 3D genome architecture of the plant pathogenic oomycetes and the influence of genome architecture on gene regulation and pathogenicity. To address this, we generated a near-complete reference genome and elucidated the 3D genome organization of the multi-host phytopathogenic oomycete Phytophthora capsici. The P. capsici genome has 17 Hi-C scaffolds with Rabl configuration, which exhibit non-random inter-chromosomal interactions. Each Hi-C scaffold separates into a core, gene-rich, transcriptionally active ‘A’ compartment and a repeat-rich, pathogenic ‘B’ compartment with a higher evolutionary rate. Topologically associated domains (TADs) are prominent with transcriptionally active, gene-rich boundaries that coincide with accessible open chromatin regions. Genes within each TAD exhibit stage-specific co-expression, indicating these motifs serve as functional regulatory units. P. capsici harbors chromatin loops similar to those in mammals. However, no CTCF binding sites are present. Instead, a strong over-representation of intergenic zf-C2H2 binding regions at loop anchors, a pattern consistent with observations in microbial eukaryotes, is observed. Altogether, these findings provide a comprehensive view of the three-dimensional genome architecture of an oomycete. A report on the 3D genome architecture of Phytophthora capsici uncovers how chromatin organization shapes gene regulation, evolution, and pathogenicity in a devastating plant pathogen.
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