Publications
2024
![Detection of genetically modified organisms using highly multiplexed amplicon sequencing](https://www.biorxiv.org/content/biorxiv/early/2023/12/23/2023.12.22.573157/F1.large.jpg?width=800&height=600&carousel=1)
Detection of genetically modified organisms using highly multiplexed amplicon sequencing
Food Control
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01 Nov 2024
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doi:10.1016/j.foodcont.2024.110670
![Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen](https://www.biorxiv.org/content/biorxiv/early/2023/09/24/2023.09.22.559077/F1.large.jpg?width=800&height=600&carousel=1)
Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen
Nature Communications
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08 Jul 2024
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doi:10.1038/s41467-024-49913-7
![Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants](https://www.biorxiv.org/content/biorxiv/early/2024/07/04/2024.07.02.601708/F3.large.jpg?width=800&height=600&carousel=1)
Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
Cold Spring Harbor Laboratory
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04 Jul 2024
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doi:10.1101/2024.07.02.601708
![Giant transposons promote strain heterogeneity in a major fungal pathogen](https://www.biorxiv.org/content/biorxiv/early/2024/06/28/2024.06.28.601215/F4.large.jpg?width=800&height=600&carousel=1)
Giant transposons promote strain heterogeneity in a major fungal pathogen
Cold Spring Harbor Laboratory
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28 Jun 2024
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doi:10.1101/2024.06.28.601215
![A highly contiguous reference genome for the Alpine ibex (<i>Capra ibex</i>)](https://www.biorxiv.org/content/biorxiv/early/2024/06/27/2024.06.24.599926/F1.large.jpg?width=800&height=600&carousel=1)
A highly contiguous reference genome for the Alpine ibex (Capra ibex)
Cold Spring Harbor Laboratory
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27 Jun 2024
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doi:10.1101/2024.06.24.599926
![Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is not caused by specific fungal communities](https://www.biorxiv.org/content/biorxiv/early/2024/04/06/2024.04.05.588363/F1.large.jpg?width=800&height=600&carousel=1)
Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is not caused by specific fungal communities
Cold Spring Harbor Laboratory
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06 Apr 2024
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doi:10.1101/2024.04.05.588363
![Million years old recombination suppression and balancing selection in a region partially linked to the mating-type locus in the invasive chestnut blight fungal pathogen<i>Cryphonectria parasitica</i>](https://www.biorxiv.org/content/biorxiv/early/2024/03/30/2024.03.29.587348/F3.large.jpg?width=800&height=600&carousel=1)
Million years old recombination suppression and balancing selection in a region partially linked to the mating-type locus in the invasive chestnut blight fungal pathogenCryphonectria parasitica
Cold Spring Harbor Laboratory
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30 Mar 2024
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doi:10.1101/2024.03.29.587348
![Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen](https://www.biorxiv.org/content/biorxiv/early/2023/03/29/2023.03.29.534750/F3.large.jpg?width=800&height=600&carousel=1)
Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen
mBio
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13 Mar 2024
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doi:10.1128/mbio.02840-23
![Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing](https://www.biorxiv.org/content/biorxiv/early/2022/12/23/2022.12.23.521735/F2.large.jpg?width=800&height=600&carousel=1)
Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
Nature Communications
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02 Mar 2024
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doi:10.1038/s41467-024-46191-1
Dimensions of genome dynamics in fungal pathogens: from fundamentals to applications
BMC Biology
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26 Jan 2024
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doi:10.1186/s12915-023-01786-w
![A systematic screen for co-option of transposable elements across the fungal kingdom](https://www.biorxiv.org/content/biorxiv/early/2023/10/23/2023.10.20.563377/F1.medium.gif)
A systematic screen for co-option of transposable elements across the fungal kingdom
Mobile DNA
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20 Jan 2024
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doi:10.1186/s13100-024-00312-1
2023
![Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen](https://www.biorxiv.org/content/biorxiv/early/2023/03/29/2023.03.29.534637/F5.large.jpg?width=800&height=600&carousel=1)
Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
Nucleic Acids Research
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24 Dec 2023
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doi:10.1093/nar/gkad1214
![Two‐speed genomes of <i>Epichloe</i> fungal pathogens show contrasting signatures of selection between species and across populations](https://onlinelibrary.wiley.com/cms/asset/15900c87-021a-47e5-9673-ff3d573007ae/mec17242-fig-0001-m.jpg)
Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations
Molecular Ecology
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12 Dec 2023
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doi:10.1111/mec.17242
![The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici](https://www.biorxiv.org/content/biorxiv/early/2023/07/17/2023.07.16.549241/F6.large.jpg?width=800&height=600&carousel=1)
The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici
Microbial Genomics
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22 Nov 2023
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doi:10.1099/mgen.0.001136
![Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen](https://www.biorxiv.org/content/biorxiv/early/2023/07/16/2023.07.14.549109/F2.large.jpg?width=800&height=600&carousel=1)
Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen
BMC Biology
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20 Nov 2023
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doi:10.1186/s12915-023-01763-3
![A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici](https://media.springernature.com/w120/springer-static/cover/journal/13104.jpg?as=webp)
A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
BMC Research Notes
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16 Nov 2023
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doi:10.1186/s13104-023-06613-7
![Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen](https://www.biorxiv.org/content/biorxiv/early/2022/05/17/2022.05.16.492091/F1.large.jpg?width=800&height=600&carousel=1)
Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen
PLOS Pathogens
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16 Nov 2023
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10.1371/journal.ppat.1011801
![Virulence Associations and Global Context of <i>AvrStb6</i> Genetic Diversity in Iranian Populations of <i>Zymoseptoria tritici</i>](https://apsjournals.apsnet.org/na101/home/literatum/publisher/aps/journals/covergifs/phyto/cover.jpg)
Virulence Associations and Global Context of AvrStb6 Genetic Diversity in Iranian Populations of Zymoseptoria tritici
Phytopathology®
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10 Nov 2023
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doi:10.1094/PHYTO-09-22-0348-R
![High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons](https://www.biorxiv.org/content/biorxiv/early/2023/07/18/2023.07.17.549274/F1.large.jpg?width=800&height=600&carousel=1)
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
Cold Spring Harbor Laboratory
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17 Jul 2023
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doi:10.1101/2023.07.17.549274
![Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen](https://www.biorxiv.org/content/biorxiv/early/2023/07/15/2023.07.14.549097/F1.large.jpg?width=800&height=600&carousel=1)
Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen
Cold Spring Harbor Laboratory
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15 Jul 2023
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doi:10.1101/2023.07.14.549097
![How genomics can help biodiversity conservation](https://www.cell.com/cms/attachment/10c60bb2-af4c-42cc-90cb-dda29c8cab23/b1.jpg)
How genomics can help biodiversity conservation
Trends in Genetics
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01 Jul 2023
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doi:10.1016/j.tig.2023.01.005
![A systemic approach allows to identify the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca/Botryosphaeria dieback](https://pathogen-genomics.org/images/pubs/monod_2023.png)
A systemic approach allows to identify the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca/Botryosphaeria dieback
Cold Spring Harbor Laboratory
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24 May 2023
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doi:10.1101/2023.05.23.541976
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
PLOS Pathogens
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12 May 2023
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doi:10.1371/journal.ppat.1011376
![Improved gene annotation of the fungal wheat pathogen<i>Zymoseptoria tritici</i>based on combined Iso-Seq and RNA-Seq evidence](https://www.biorxiv.org/content/biorxiv/early/2023/04/28/2023.04.26.537486/F4.large.jpg)
Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence
Cold Spring Harbor Laboratory
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28 Apr 2023
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doi:10.1101/2023.04.26.537486
![Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics](https://journals.asm.org/cms/10.1128/spectrum.02513-22/asset/7c8dbf9a-c852-4c77-968a-914b40ea236a/assets/images/medium/spectrum.02513-22-f001.gif)
Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics
Microbiology Spectrum
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13 Apr 2023
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doi:10.1128/spectrum.04443-22
Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus
PLOS Biology
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11 Apr 2023
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doi:10.1371/journal.pbio.3002052
![A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41467-023-36674-y/MediaObjects/41467_2023_36674_Fig2_HTML.png?as=webp)
A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
Nature Communications
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24 Feb 2023
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doi:10.1038/s41467-023-36674-y
![Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/9970103/bin/ppat.1011130.g007.jpg)
Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen
PLOS Pathogens
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14 Feb 2023
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doi:10.1371/journal.ppat.1011130
A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici
PLOS ONE
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06 Feb 2023
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doi:10.1371/journal.pone.0281181
![Genome Evolution in Fungal Plant Pathogens: From Populations to Kingdom-Wide Dynamics](https://m.media-amazon.com/images/I/41SCSh55CjL.jpg)
Genome Evolution in Fungal Plant Pathogens: From Populations to Kingdom-Wide Dynamics
The Mycota
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01 Jan 2023
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doi:10.1007/978-3-031-29199-9_5
2022
![Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome](https://journals.asm.org/cms/10.1128/spectrum.02513-22/asset/7c8dbf9a-c852-4c77-968a-914b40ea236a/assets/images/medium/spectrum.02513-22-f001.gif)
Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome
Microbiology Spectrum
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21 Dec 2022
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doi:10.1128/spectrum.02513-22
![Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen](https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12915-022-01422-z/MediaObjects/12915_2022_1422_Fig5_HTML.png?as=webp)
Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen
BMC Biology
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08 Oct 2022
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doi:10.1186/s12915-022-01422-z
![Unraveling coevolutionary dynamics using ecological genomics](https://ars.els-cdn.com/content/image/1-s2.0-S0168952522001160-gr1.jpg)
Unraveling coevolutionary dynamics using ecological genomics
Trends in Genetics
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01 Oct 2022
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doi:10.1016/j.tig.2022.05.008
![Global diversification of the common moonwort ferns (<i>Botrychium lunaria</i> group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts](https://www.biorxiv.org/content/biorxiv/early/2022/09/28/2022.09.28.509846/F1.large.jpg?width=800&height=600&carousel=1)
Global diversification of the common moonwort ferns (Botrychium lunaria group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts
Cold Spring Harbor Laboratory
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28 Sep 2022
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doi:10.1101/2022.09.28.509846
![Genome of Malassezia arunalokei and Its Distribution on Facial Skin](https://journals.asm.org/cms/10.1128/spectrum.00506-22/asset/2f734217-262a-450c-a686-e5c671ead678/assets/images/medium/spectrum.00506-22-f004.gif)
Genome of Malassezia arunalokei and Its Distribution on Facial Skin
Microbiology Spectrum
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29 Jun 2022
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doi:10.1128/spectrum.00506-22
![Organic acids and glucose prime late-stage fungal biotrophy in maize](https://www.science.org/cms/10.1126/science.abo2401/asset/ee4f671d-5281-417b-91f4-bd63debd404d/assets/images/large/science.abo2401-f1.jpg)
Organic acids and glucose prime late-stage fungal biotrophy in maize
Science
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10 Jun 2022
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doi:10.1126/science.abo2401
![The population genetics of adaptation through copy number variation in a fungal plant pathogen](https://onlinelibrary.wiley.com/cms/asset/cefd2651-d368-4311-b0f1-1c8d5f24d106/mec16435-fig-0001-m.jpg)
The population genetics of adaptation through copy number variation in a fungal plant pathogen
Molecular Ecology
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05 Apr 2022
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doi:10.1111/mec.16435
![The era of reference genomes in conservation genomics](https://ars.els-cdn.com/content/image/1-s2.0-S016953472100313X-gr1.jpg)
The era of reference genomes in conservation genomics
Trends in Ecology & Evolution
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01 Mar 2022
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doi:10.1016/j.tree.2021.11.008
![A devil's bargain with transposable elements in plant pathogens](https://ars.els-cdn.com/content/image/1-s2.0-S0168952521002298-gr1.jpg)
A devil's bargain with transposable elements in plant pathogens
Trends in Genetics
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01 Mar 2022
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doi:10.1016/j.tig.2021.08.005
![Temporal changes in pathogen diversity in a perennial plant–pathogen–hyperparasite system](https://onlinelibrary.wiley.com/cms/asset/78ac288f-eac7-4c3e-81fb-4b6ef8e7a35e/mec16386-fig-0001-m.jpg)
Temporal changes in pathogen diversity in a perennial plant–pathogen–hyperparasite system
Molecular Ecology
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16 Feb 2022
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doi:10.1111/mec.16386
Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat
PLOS Pathogens
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06 Jan 2022
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doi:10.1371/journal.ppat.1010149
![High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees](https://minio.scielo.br/documentstore/1678-4685/hfKvwbdD9dqHy4xPSrCTDFv/178177a297130f3f85bc84c3dfec869cf10dff63.jpg)
High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees
Genetics and Molecular Biology
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01 Jan 2022
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doi:10.1590/1678-4685-GMB-2021-0051
![Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population](https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/gigascience/11/10.1093_gigascience_giac090/2/giac090fig1.jpeg?Expires=1695154937&Signature=E9CWWeJLhEbhyR54Q9D5cwIFsvwqhImAt9XaSiEbhMbD5fNE0hMnkHZQ7J~ANvgFfW-nmoLg4Oi9ixZ0Z3gDV6BuUo3yiyub-Yj2Nx-C9y7eThjLQ4UB5S~eDxrkTShJpctbgW7NxHUqwK0Pvz9F5RuAGaphX9owimEFuJZUh2Om348Lic8ShLqJoStTJdGPTKARh~vmQhaKepZNUsbWdDsIr6tjnJyFhoNuWK~PHz05kyyCfc9iWj87zXo2EDU8DiMwTs9LUA2uGGrlgGxn0hOe3ozAe7xtDIIq5YbOzHDLkFI5Pw5QZQOyp3Cje0mw8q8w4LbLU3G6-iUFR3kKTQ__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
GigaScience
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01 Jan 2022
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doi:10.1093/gigascience/giac090
2021
![Screening of grapevine red blotch virus in two European ampelographic collections](https://media.springernature.com/lw685/springer-static/image/art%3A10.1007%2Fs42161-021-00952-9/MediaObjects/42161_2021_952_Fig1_HTML.jpg?as=webp)
Screening of grapevine red blotch virus in two European ampelographic collections
Journal of Plant Pathology
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12 Nov 2021
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doi:10.1007/s42161-021-00952-9
![Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi](https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/mbe/39/1/10.1093_molbev_msab323/1/msab323f1.jpeg?Expires=1695154882&Signature=EMVbdDgFCep4g-MrmvLsRpCM5eXoVaFQXAFC0dYhWDmtv3pQT9QQAUo8uZqIRNwhanJ8bTQicCaW4ZBbFcEF~Idv0e-nrvNFmtB0aFp8tlfG6OaBYX0Bjie1Pdg2xb7A6~nBsbqvF3AghPoGjvigE38clbWJ3ulh-K2~8m3n-eErUEanX2NmlbBeBrCT5jwTjgih7olJ6L82YXhbdfqb7x4T1f-~8Q7Z-UswB0Oh3VU-EbDPKBep03b9V-0KKLPqf82smKuNZiDEIkNBreUNgmAYAulYMwjls-zmDo~U-8EOsqGHBy6Ym6s5wkIjklTe2O1UizUiz91yjeVrzMAcqA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi
Molecular Biology and Evolution
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09 Nov 2021
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doi:10.1093/molbev/msab323
![Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici](https://www.microbiologyresearch.org/docserver/fulltext/mgen/7/10/mgen000678-f1.gif)
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici
Microbial Genomics
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01 Nov 2021
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doi:10.1099/mgen.0.000678
![Soil composition and plant genotype determine benzoxazinoid‐mediated plant–soil feedbacks in cereals](https://onlinelibrary.wiley.com/cms/asset/fea555ab-0adc-44ea-8e87-5148beefba86/pce14184-fig-0002-m.jpg)
Soil composition and plant genotype determine benzoxazinoid‐mediated plant–soil feedbacks in cereals
Plant, Cell & Environment
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23 Sep 2021
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doi:10.1111/pce.14184
![A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen](https://iiif.elifesciences.org/lax/69249%2Felife-69249-fig6-v1.tif/full/,1500/0/default.jpg)
A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
eLife
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16 Sep 2021
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doi:10.7554/eLife.69249
![Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus <scp><i>Cenococcum geophilum</i></scp>](https://ami-journals.onlinelibrary.wiley.com/cms/asset/c2cde51d-2088-4a5d-8e8b-e55329b28add/emi15752-fig-0001-m.jpg)
Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum
Environmental Microbiology
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15 Sep 2021
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doi:10.1111/1462-2920.15752
![Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen](https://www.microbiologyresearch.org/docserver/fulltext/mgen/7/8/mgen000540-f1.gif)
Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen
Microbial Genomics
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31 Aug 2021
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doi:10.1099/mgen.0.000540
![Transcriptome‐wide SNPs for <i>Botrychium lunaria</i> ferns enable fine‐grained analysis of ploidy and population structure](https://onlinelibrary.wiley.com/cms/asset/26b905bd-e8ba-42b8-a557-3538d34b87d4/men13478-fig-0001-m.png)
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure
Molecular Ecology Resources
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07 Aug 2021
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doi:10.1111/1755-0998.13478
![A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics](https://onlinelibrary.wiley.com/cms/asset/54ad25ce-4591-4158-a7c1-f85aba439e79/men13452-fig-0001-m.jpg)
A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics
Molecular Ecology Resources
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07 Jul 2021
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doi:10.1111/1755-0998.13452
![Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41467-021-23862-x/MediaObjects/41467_2021_23862_Fig1_HTML.png?as=webp)
Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen
Nature Communications
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10 Jun 2021
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doi:10.1038/s41467-021-23862-x
![A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire](https://onlinelibrary.wiley.com/cms/asset/65e27dd2-6e97-461e-8529-44c3c2e7fcd2/aje12888-fig-0003-m.jpg)
A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire
African Journal of Ecology
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09 Jun 2021
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doi:10.1111/aje.12888
![Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen](https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs12864-021-07691-2/MediaObjects/12864_2021_7691_Fig1_HTML.png?as=webp)
Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
BMC Genomics
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27 May 2021
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doi:10.1186/s12864-021-07691-2
![Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection](https://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-021-02843-7/MediaObjects/10681_2021_2843_Fig2_HTML.png?as=webp)
Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection
Euphytica
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11 May 2021
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doi:10.1007/s10681-021-02843-7
![Whole-genome analyses of 286 Magnaporthe oryzae genomes suggest that an independent introduction of a global pandemic lineage is at the origin of the Zambia wheat blast outbreak](https://pathogen-genomics.org/images/pubs/croll_zenodo.png)
Whole-genome analyses of 286 Magnaporthe oryzae genomes suggest that an independent introduction of a global pandemic lineage is at the origin of the Zambia wheat blast outbreak
Zenodo
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01 Apr 2021
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doi:10.5281/zenodo.4655959
![Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe](https://iiif.elifesciences.org/lax/56279%2Felife-56279-fig1-v1.tif/full/,1500/0/default.jpg)
Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
eLife
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05 Mar 2021
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doi:10.7554/eLife.56279
![Fusarium: more than a node or a foot-shaped basal cell](https://ars.els-cdn.com/content/image/1-s2.0-S0166061621000038-gr6.jpg)
Fusarium: more than a node or a foot-shaped basal cell
Studies in Mycology
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01 Mar 2021
·
doi:10.1016/j.simyco.2021.100116
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The ISME Journal
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Persoonia - Molecular Phylogeny and Evolution of Fungi
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01 Jan 2021
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Food Chemistry, Function and Analysis
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Tackling microbial threats in agriculture with integrative imaging and computational approaches
Computational and Structural Biotechnology Journal
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Molecular Ecology
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mSphere
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G3 Genes|Genomes|Genetics
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Evolutionary Applications
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BMC Genomics
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Current Opinion in Plant Biology
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PLOS Pathogens
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Heredity
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Nature Communications
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BMC Biology
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2019
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Genome Biology and Evolution
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Environmental Microbiology
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Phytopathology®
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Applied and Environmental Microbiology
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2018
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mBio
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Current Opinion in Microbiology
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Molecular Plant Pathology
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Annual Review of Phytopathology
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Annual Review of Phytopathology
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BMC Biology
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16 Jul 2018
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Genome Biology and Evolution
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Molecular Ecology
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Genome Biology and Evolution
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Molecular Ecology
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27 Apr 2018
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New Phytologist
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25 Apr 2018
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Frontiers in Microbiology
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06 Apr 2018
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BMC Biology
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11 Jan 2018
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Molecular Microbiology
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2017
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Molecular Plant Pathology
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11 Dec 2017
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Fungal Genetics and Biology
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Evolutionary Applications
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27 Oct 2017
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Cold Spring Harbor Laboratory
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16 Oct 2017
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Molecular Biology and Evolution
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Molecular Plant-Microbe Interactions®
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Trends in Ecology & Evolution
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New Phytologist
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06 Feb 2017
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Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogenZymoseptoria tritici
Molecular Plant Pathology
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05 Feb 2017
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doi:10.1111/mpp.12515
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Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution
Frontiers in Plant Science
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03 Feb 2017
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doi:10.3389/fpls.2017.00119
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A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
The ISME Journal
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24 Jan 2017
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doi:10.1038/ismej.2016.196
2016
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Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations
Molecular Ecology
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30 Nov 2016
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doi:10.1111/mec.13916
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Maize susceptibility to Ustilago maydis is influenced by genetic and chemical perturbation of carbohydrate allocation
Molecular Plant Pathology
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14 Nov 2016
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doi:10.1111/mpp.12486
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Chloroplast‐associated metabolic functions influence the susceptibility of maize to Ustilago maydis
Molecular Plant Pathology
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14 Nov 2016
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doi:10.1111/mpp.12485
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The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat
mBio
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02 Nov 2016
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doi:10.1128/mBio.01231-16
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The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems
Molecular Ecology
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24 Oct 2016
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doi:10.1111/mec.13870
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What the population genetic structures of host and pathogen tell us about disease evolution
New Phytologist
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13 Oct 2016
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doi:10.1111/nph.14203
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Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
BMC Biology
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03 Oct 2016
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doi:10.1186/s12915-016-0309-7
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Evolution in the absence of sex: Ideas revisited in the post‐genomics age (retrospective on DOI 10.1002/bies.201300155)
BioEssays
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19 Sep 2016
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doi:10.1002/bies.201600195
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Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact
Molecular Ecology
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26 Aug 2016
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doi:10.1111/mec.13751
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The putative phospholipase Lip2 counteracts oxidative damage and influences the virulence of Ustilago maydis
Molecular Plant Pathology
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21 Apr 2016
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doi:10.1111/mpp.12391
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Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation
mBio
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02 Mar 2016
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doi:10.1128/mBio.01862-15
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Comparative transcriptomic analyses of Z ymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles
Molecular Plant Pathology
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08 Feb 2016
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doi:10.1111/mpp.12333
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QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici
Heredity
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13 Jan 2016
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doi:10.1038/hdy.2015.111
2015
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Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A
BMC Microbiology
·
09 Oct 2015
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doi:10.1186/s12866-015-0532-3
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The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen
Genetics
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21 Sep 2015
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doi:10.1534/genetics.115.180968
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QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici
Fungal Genetics and Biology
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01 Jul 2015
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doi:10.1016/j.fgb.2015.05.001
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Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis
Mycoses
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10 Feb 2015
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doi:10.1111/myc.12296
2014
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Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic FungusZymoseptoria tritici
G3 Genes|Genomes|Genetics
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01 Dec 2014
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doi:10.1534/g3.114.015289
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Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution
mBio
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29 Aug 2014
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doi:10.1128/mBio.01494-14
Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
PLoS Genetics
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19 Jun 2014
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doi:10.1371/journal.pgen.1004438
![The evolving fungal genome](https://ars.els-cdn.com/content/image/1-s2.0-S1749461314000025-gr2.jpg)
The evolving fungal genome
Fungal Biology Reviews
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01 May 2014
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doi:10.1016/j.fbr.2014.02.001
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Hitchhiking Selection Is Driving Intron Gain in a Pathogenic Fungus
Molecular Biology and Evolution
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07 Apr 2014
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doi:10.1093/molbev/msu123
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Learn from the fungi: Adaptive evolution without sex in fungal pathogens (comment on DOI 10.1002/bies.201300155)
BioEssays
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05 Mar 2014
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doi:10.1002/bies.201400030
2013
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An assay for quantitative virulence in R hynchosporium commune reveals an association between effector genotype and virulence
Plant Pathology
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06 Aug 2013
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doi:10.1111/ppa.12111
Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen
PLoS Genetics
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13 Jun 2013
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doi:10.1371/journal.pgen.1003567
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Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen
Molecular Biology and Evolution
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20 Mar 2013
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doi:10.1093/molbev/mst041
2012
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Population genetic structure of Mycosphaerella graminicola and Quinone Outside Inhibitor (QoI) resistance in the Czech Republic
European Journal of Plant Pathology
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14 Sep 2012
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doi:10.1007/s10658-012-0080-8
The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens
PLoS Pathogens
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26 Apr 2012
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doi:10.1371/journal.ppat.1002608
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What if esca disease of grapevine were not a fungal disease?
Fungal Diversity
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24 Apr 2012
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doi:10.1007/s13225-012-0171-z
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Intron Gains and Losses in the Evolution of Fusarium and Cryptococcus Fungi
Genome Biology and Evolution
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01 Jan 2012
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doi:10.1093/gbe/evs091
2011
![Evidence for Extensive Recent Intron Transposition in Closely Related Fungi](https://ars.els-cdn.com/content/image/1-s2.0-S0960982211012024-gr3.jpg)
Evidence for Extensive Recent Intron Transposition in Closely Related Fungi
Current Biology
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01 Dec 2011
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doi:10.1016/j.cub.2011.10.041
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The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont
New Phytologist
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16 Nov 2011
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doi:10.1111/j.1469-8137.2011.03948.x
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A cryptic heterogametic transition revealed by sex‐linked DNA markers in Palearctic green toads
Journal of Evolutionary Biology
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21 Feb 2011
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doi:10.1111/j.1420-9101.2011.02239.x
2010
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Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner
Annual Review of Genetics
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01 Dec 2010
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doi:10.1146/annurev-genet-102108-134239
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Segregation in a Mycorrhizal Fungus Alters Rice Growth and Symbiosis-Specific Gene Transcription
Current Biology
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01 Jul 2010
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doi:10.1016/j.cub.2010.05.031
2009
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High-Level Molecular Diversity of Copper-Zinc Superoxide Dismutase Genes among and within Species of Arbuscular Mycorrhizal Fungi
Applied and Environmental Microbiology
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01 Apr 2009
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doi:10.1128/AEM.01974-08
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Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus
BMC Evolutionary Biology
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01 Jan 2009
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doi:10.1186/1471-2148-9-13
2008
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Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus Glomus intraradices
New Phytologist
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24 Dec 2008
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doi:10.1111/j.1469-8137.2008.02726.x
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Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics
New Phytologist
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15 Oct 2008
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doi:10.1111/j.1469-8137.2008.02602.x
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Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices
New Phytologist
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20 Feb 2008
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doi:10.1111/j.1469-8137.2008.02381.x
2007
![Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population](https://journals.asm.org/cms/10.1128/AEM.01574-06/asset/ea9539ee-81a3-4f56-8050-bfc8b7d526f5/assets/graphic/zam0010773710001.jpeg)
Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population
Applied and Environmental Microbiology
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01 Jan 2007
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doi:10.1128/AEM.01574-06
2005
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Genetic variability in a population of arbuscular mycorrhizal fungi causes variation in plant growth
Ecology Letters
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22 Nov 2005
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doi:10.1111/j.1461-0248.2005.00853.x