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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781603/ https://www.ncbi.nlm.nih.gov/pubmed/33337321 http://dx.doi.org/10.7554/eLife.62208 |
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author | Cook, David E Kramer, H Martin Torres, David E Seidl, Michael F Thomma, Bart P H J |
author_facet | Cook, David E Kramer, H Martin Torres, David E Seidl, Michael F Thomma, Bart P H J |
author_sort | Cook, David E |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-7781603 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-77816032021-01-06 A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen Cook, David E Kramer, H Martin Torres, David E Seidl, Michael F Thomma, Bart P H J eLife Evolutionary Biology 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. eLife Sciences Publications, Ltd 2020-12-18 /pmc/articles/PMC7781603/ /pubmed/33337321 http://dx.doi.org/10.7554/eLife.62208 Text en © 2020, Cook et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Evolutionary Biology Cook, David E Kramer, H Martin Torres, David E Seidl, Michael F Thomma, Bart P H J A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen |
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 | Evolutionary Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781603/ https://www.ncbi.nlm.nih.gov/pubmed/33337321 http://dx.doi.org/10.7554/eLife.62208 |
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