A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

Abstract
Data availability
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Abstract

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.

Data availability

The sequencing data for this project are accessible from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA592220.

The following data sets were generated

1. Cook DE
2. Kramer HM
3. Torres DE
4. Seidl MF
5. Thomma BPHJ
(2020) A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
NCBI Sequence Read Archive, BioProject PRJNA592220.

https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA592220

The following previously published data sets were used

(2015) ingle-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
GenBank, GCA_000400815.2.

https://www.ncbi.nlm.nih.gov/assembly/GCA_000400815.2

Article and author information

Author details

David E Cook

Department of Plant Pathology, Kansas State University, Manhattan, United States

For correspondence
decook@ksu.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2719-4701
H Martin Kramer

Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands

Competing interests
The authors declare that no competing interests exist.
David E Torres

Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands

Competing interests
The authors declare that no competing interests exist.
Michael F Seidl

Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands

Competing interests
The authors declare that no competing interests exist.
Bart PHJ Thomma

Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands

For correspondence
bart.thomma@wur.nl

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4125-4181

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek

Michael F Seidl
Bart PHJ Thomma

European Molecular Biology Organization (Postdoctoral fellowship EMBO, ALTF 969-2013)

David E Cook

Human Frontier Science Program (Postdoctoral Fellowship HFSP, LT000627/2014-L)

David E Cook

Deutsche Forschungsgemeinschaft

Bart PHJ Thomma

Conacyt

David E Torres

United States Department of Agriculture

David E Cook

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.