Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures
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:...
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| Format: | Article |
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2023-01-01
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| Series: | Peer Community Journal |
| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.227/ |
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| author | Clairet, Colin Lapalu, Nicolas Simon, Adeline Soyer, Jessica L. Viaud, Muriel Zehraoui, Enric Dalmais, Berengère Fudal, Isabelle Ponts, Nadia |
| author_facet | Clairet, Colin Lapalu, Nicolas Simon, Adeline Soyer, Jessica L. Viaud, Muriel Zehraoui, Enric Dalmais, Berengère Fudal, Isabelle Ponts, Nadia |
| author_sort | Clairet, Colin |
| collection | DOAJ |
| description | 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.
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| format | Article |
| id | doaj-art-0f8a08aa675b42a19462eb5d659ed8ec |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-0f8a08aa675b42a19462eb5d659ed8ec2025-02-07T10:16:49ZengPeer Community InPeer Community Journal2804-38712023-01-01310.24072/pcjournal.22710.24072/pcjournal.227Nucleosome patterns in four plant pathogenic fungi with contrasted genome structuresClairet, Colin0https://orcid.org/0000-0003-4546-6763Lapalu, Nicolas1https://orcid.org/0000-0002-9773-4611Simon, Adeline2https://orcid.org/0000-0002-0020-6442Soyer, Jessica L.3Viaud, Muriel4Zehraoui, Enric5https://orcid.org/0000-0002-9040-2198Dalmais, Berengère6Fudal, Isabelle7https://orcid.org/0000-0002-9105-9432Ponts, Nadia8https://orcid.org/0000-0002-3205-6776Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France; 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, GermanyUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceINRAE, MycSA, F-33882 Villenave d’Ornon, 33140, FranceUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceUniversité Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, FranceINRAE, MycSA, F-33882 Villenave d’Ornon, 33140, FranceFungal 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.227/ |
| spellingShingle | 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 |
| title | Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| title_full | Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| title_fullStr | Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| title_full_unstemmed | Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| title_short | Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| title_sort | nucleosome patterns in four plant pathogenic fungi with contrasted genome structures |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.227/ |
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