Genomics

Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

10.24072/pcjournal.227 - Peer Community Journal, Volume 3 (2023), article no. e13.

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Fungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.

Published online:
DOI: 10.24072/pcjournal.227
Clairet, Colin 1; Lapalu, Nicolas 1; Simon, Adeline 1; Soyer, Jessica L. 1, 2; Viaud, Muriel 1; Zehraoui, Enric 3; Dalmais, Berengère 1; Fudal, Isabelle 1; Ponts, Nadia 3

1 Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
2 Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, and Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
3 INRAE, MycSA, F-33882 Villenave d’Ornon, 33140, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     title = {Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures},
     journal = {Peer Community Journal},
     eid = {e13},
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Clairet, Colin; Lapalu, Nicolas; Simon, Adeline; Soyer, Jessica L.; Viaud, Muriel; Zehraoui, Enric; Dalmais, Berengère; Fudal, Isabelle; Ponts, Nadia. Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures. Peer Community Journal, Volume 3 (2023), article  no. e13. doi : 10.24072/pcjournal.227. https://peercommunityjournal.org/articles/10.24072/pcjournal.227/

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100014

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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