A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evo...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2020-12-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/62208 |
| _version_ | 1811201425665949696 |
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| author | David E Cook H Martin Kramer David E Torres Michael F Seidl Bart P H J Thomma |
| author_facet | David E Cook H Martin Kramer David E Torres Michael F Seidl Bart P H J Thomma |
| author_sort | David E Cook |
| collection | DOAJ |
| description | Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions. |
| first_indexed | 2024-04-12T02:20:19Z |
| format | Article |
| id | doaj.art-ba24bc4cb3e34b60bbdb76846a0513d0 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T02:20:19Z |
| publishDate | 2020-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-ba24bc4cb3e34b60bbdb76846a0513d02022-12-22T03:52:08ZengeLife Sciences Publications LtdeLife2050-084X2020-12-01910.7554/eLife.62208A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogenDavid E Cook0https://orcid.org/0000-0002-2719-4701H Martin Kramer1David E Torres2Michael F Seidl3Bart P H J Thomma4https://orcid.org/0000-0003-4125-4181Department of Plant Pathology, Kansas State University, Manhattan, United States; Laboratory of Phytopathology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Phytopathology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands; Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, NetherlandsLaboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands; Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, NetherlandsLaboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands; University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, GermanyGenomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions.https://elifesciences.org/articles/62208verticillium dahliaechromatinepigenomeDNA methylationhistone modificationatac sequencing |
| spellingShingle | David E Cook H Martin Kramer David E Torres Michael F Seidl Bart P H J Thomma A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen eLife verticillium dahliae chromatin epigenome DNA methylation histone modification atac sequencing |
| title | A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| title_full | A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| title_fullStr | A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| title_full_unstemmed | A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| title_short | A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| title_sort | unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
| topic | verticillium dahliae chromatin epigenome DNA methylation histone modification atac sequencing |
| url | https://elifesciences.org/articles/62208 |
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