Evolutionary genomics of pathogens Croll lab at University of Neuchatel

Publications

Highlight bioRxiv Review TEs Zymoseptoria Microbiome Mycorrhizal fungi Wheat blast Human pathogens GMO detection Conservation genomics

2025

An inversion polymorphism under balancing selection, involving giant mobile elements, in an invasive fungal pathogen
An inversion polymorphism under balancing selection, involving giant mobile elements, in an invasive fungal pathogen
Fanny E Hartmann, Ricardo C Rodríguez de la Vega, Arthur Demené, Thomas Badet, Jean-Philippe Vernadet, …, Lea Stauber, Daniel Croll, Simone Prospero, Cyril Dutech, Tatiana Giraud
Molecular Biology and Evolution  ·  05 Feb 2025  ·  doi:10.1093/molbev/msaf026
Wheat infection by<i>Fusarium graminearum</i>species complex members is facilitated by a transcriptionally conserved non-ribosomal peptide synthetase gene cluster
Wheat infection byFusarium graminearumspecies complex members is facilitated by a transcriptionally conserved non-ribosomal peptide synthetase gene cluster
Sabina Moser Tralamazza, Mikkel Rank Nielsen, Leen Nanchira Abraham, Anna K. Atanasoff-Kardjalieff, Gaetan Glauser, Jens Laurids Sørensen, Lena Studt-Reinhold, Benedito Corrêa, Daniel Croll
Cold Spring Harbor Laboratory  ·  25 Jan 2025  ·  doi:10.1101/2025.01.24.634825
bioRxiv
A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom
A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom
Thomas Badet, Daniel Croll
Cold Spring Harbor Laboratory  ·  14 Jan 2025  ·  doi:10.1101/2025.01.10.632494
bioRxiv TEs
Global diversification of the common moonwort ferns (<i>Botrychium lunaria</i> group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts
Global diversification of the common moonwort ferns (Botrychium lunaria group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts
Vinciane Mossion, Erik Koenen, Jason Grant, Daniel Croll, Donald R Farrar, Michael Kessler
Annals of Botany  ·  11 Jan 2025  ·  doi:10.1093/aob/mcae228
Identifying the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca disease
Identifying the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca disease
Valérie Hofstetter, Vinciane Monod, Matthieu Wilhelm, Olivier Viret, Katia Gindro, Daniel Croll, Vivian Zufferey
OENO One  ·  08 Jan 2025  ·  doi:10.20870/oeno-one.2025.59.1.7659
Microbiome

2024

Rapid and In-situ Detection of Biological Agents via Near-Infrared Spectroscopy and Cloud-Powered Neural Networks
Rapid and In-situ Detection of Biological Agents via Near-Infrared Spectroscopy and Cloud-Powered Neural Networks
Chloé Leseigneur, Isabelle Radgen-Morvant, César Metzger, Pierre Esseiva, Daniel Croll, Pascal Miéville
Cold Spring Harbor Laboratory  ·  15 Nov 2024  ·  doi:10.1101/2024.11.15.623740
bioRxiv
Detection of genetically modified organisms using highly multiplexed amplicon sequencing
Detection of genetically modified organisms using highly multiplexed amplicon sequencing
C. Sarai Reyes-Avila, Dominique Waldvogel, Nicolas Pradervand, Sylvain Aubry, Daniel Croll
Food Control  ·  01 Nov 2024  ·  doi:10.1016/j.foodcont.2024.110670
GMO detection
Revisiting the evolution and function of NIP2 parologs in the<i>Rhynchosporium spp.</i>complex
Revisiting the evolution and function of NIP2 parologs in theRhynchosporium spp.complex
Reynaldi Darma, Daniel S. Yu, Megan A. Outram, Yi-Chang Sung, Erin H. Hill, …, Simon J. Williams, Ben Ovenden, Andrew Milgate, Peter S. Solomon, Megan C. McDonald
Cold Spring Harbor Laboratory  ·  18 Oct 2024  ·  doi:10.1101/2024.10.15.618441
bioRxiv
Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogen<i>Zymoseptoria tritici</i>
Diversification, loss, and virulence gains of the major effector AvrStb6 during continental spread of the wheat pathogenZymoseptoria tritici
Ana Margarida Sampaio, Sabina Moser Tralamazza, Faharidine Mohamadi, Yannick De Oliveira, Jérôme Enjalbert, Cyrille Saintenac, Daniel Croll
Cold Spring Harbor Laboratory  ·  15 Oct 2024  ·  doi:10.1101/2024.10.12.618020
bioRxiv TEs
Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
Caio A Leal-Dutra, Joel Vizueta, Tobias Baril, Pepijn W Kooij, Asta Rødsgaard-Jørgensen, Benjamin H Conlon, Daniel Croll, Jonathan Z Shik
Molecular Biology and Evolution  ·  17 Sep 2024  ·  doi:10.1093/molbev/msae197
TEs
Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen
Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen
Sabina Moser Tralamazza, Emile Gluck-Thaler, Alice Feurtey, Daniel Croll
Nature Communications  ·  08 Jul 2024  ·  doi:10.1038/s41467-024-49913-7
Highlight TEs Zymoseptoria
Giant transposons promote strain heterogeneity in a major fungal pathogen
Giant transposons promote strain heterogeneity in a major fungal pathogen
Emile Gluck-Thaler, Adrian Forsythe, Charles Puerner, Jason E. Stajich, Daniel Croll, Robert A. Cramer, Aaron A. Vogan
Cold Spring Harbor Laboratory  ·  28 Jun 2024  ·  doi:10.1101/2024.06.28.601215
bioRxiv TEs
A highly contiguous reference genome for the Alpine ibex (<i>Capra ibex</i>)
A highly contiguous reference genome for the Alpine ibex (Capra ibex)
F. Gözde Çilingir, Fabio Landuzzi, Alice Brambilla, Debora Charrance, Federica Furia, …, Bruno Bassano, Stefano Gustincich, Daniel Croll, Luca Pandolfini, Christine Grossen
Cold Spring Harbor Laboratory  ·  27 Jun 2024  ·  doi:10.1101/2024.06.24.599926
Conservation genomics
Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is not caused by specific fungal communities
Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is not caused by specific fungal communities
Vinciane Monod, Valérie Hofstetter, Olivier Viret, Vivian Zufferey, Katia Gindro, Daniel Croll
Cold Spring Harbor Laboratory  ·  06 Apr 2024  ·  doi:10.1101/2024.04.05.588363
bioRxiv Microbiome
Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen
Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen
Leen Nanchira Abraham, Ursula Oggenfuss, Daniel Croll
mBio  ·  13 Mar 2024  ·  doi:10.1128/mbio.02840-23
Highlight TEs Zymoseptoria
Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
Reda Amezrou, Aurélie Ducasse, Jérôme Compain, Nicolas Lapalu, Anais Pitarch, …, Gert H. J. Kema, Daniel Croll, Joëlle Amselem, Andrea Sanchez-Vallet, Thierry C. Marcel
Nature Communications  ·  02 Mar 2024  ·  doi:10.1038/s41467-024-46191-1
Highlight Zymoseptoria
Dimensions of genome dynamics in fungal pathogens: from fundamentals to applications
Dimensions of genome dynamics in fungal pathogens: from fundamentals to applications
Daniel Croll
BMC Biology  ·  26 Jan 2024  ·  doi:10.1186/s12915-023-01786-w
Review
A systematic screen for co-option of transposable elements across the fungal kingdom
A systematic screen for co-option of transposable elements across the fungal kingdom
Ursula Oggenfuss, Thomas Badet, Daniel Croll
Mobile DNA  ·  20 Jan 2024  ·  doi:10.1186/s13100-024-00312-1
TEs bioRxiv

2023

Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
Thomas Badet, Sabina Moser Tralamazza, Alice Feurtey, Daniel Croll
Nucleic Acids Research  ·  24 Dec 2023  ·  doi:10.1093/nar/gkad1214
Highlight TEs Zymoseptoria
Two‐speed genomes of <i>Epichloe</i> fungal pathogens show contrasting signatures of selection between species and across populations
Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations
Artemis D. Treindl, Jessica Stapley, Daniel Croll, Adrian Leuchtmann
Molecular Ecology  ·  12 Dec 2023  ·  doi:10.1111/mec.17242
The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici
The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici
Hanna M. Glad, Sabina Moser Tralamazza, Daniel Croll
Microbial Genomics  ·  22 Nov 2023  ·  doi:10.1099/mgen.0.001136
Zymoseptoria
Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen
Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen
Leen Nanchira Abraham, Daniel Croll
BMC Biology  ·  20 Nov 2023  ·  doi:10.1186/s12915-023-01763-3
Highlight Zymoseptoria
A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
Tobias Baril, Daniel Croll
BMC Research Notes  ·  16 Nov 2023  ·  doi:10.1186/s13104-023-06613-7
TEs Zymoseptoria
Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen
Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen
Anik Dutta, Bruce A. McDonald, Daniel Croll
PLOS Pathogens  ·  16 Nov 2023  ·  10.1371/journal.ppat.1011801
Highlight Zymoseptoria
Virulence Associations and Global Context of <i>AvrStb6</i> Genetic Diversity in Iranian Populations of <i>Zymoseptoria tritici</i>
Virulence Associations and Global Context of AvrStb6 Genetic Diversity in Iranian Populations of Zymoseptoria tritici
Sepideh Hatami Rad, Leila Ebrahimi, Daniel Croll
Phytopathology®  ·  10 Nov 2023  ·  doi:10.1094/PHYTO-09-22-0348-R
Zymoseptoria
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons
Luzia Stalder, Monika Maurhofer, Daniel Croll
Cold Spring Harbor Laboratory  ·  17 Jul 2023  ·  doi:10.1101/2023.07.17.549274
bioRxiv Microbiome Zymoseptoria
Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen
Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen
Simone Fouché, Ursula Oggenfuss, Bruce A. McDonald, Daniel Croll
Cold Spring Harbor Laboratory  ·  15 Jul 2023  ·  doi:10.1101/2023.07.14.549097
bioRxiv TEs Zymoseptoria
How genomics can help biodiversity conservation
How genomics can help biodiversity conservation
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, …, David R. Vieites, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
Trends in Genetics  ·  01 Jul 2023  ·  doi:10.1016/j.tig.2023.01.005
Conservation genomics Review
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
Reda Amezrou, Colette Audéon, Jérôme Compain, Sandrine Gélisse, Aurélie Ducasse, …, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry C. Marcel
PLOS Pathogens  ·  12 May 2023  ·  doi:10.1371/journal.ppat.1011376
Zymoseptoria
Improved gene annotation of the fungal wheat pathogen<i>Zymoseptoria tritici</i>based on combined Iso-Seq and RNA-Seq evidence
Improved gene annotation of the fungal wheat pathogenZymoseptoria triticibased on combined Iso-Seq and RNA-Seq evidence
Nicolas Lapalu, Lucie Lamothe, Yohann Petit, Anne Genissel, Camille Delude, …, Jason Rudd, Eva Stukenbrock, Daniel Croll, Gabriel Scalliet, Marc-Henri Lebrun
Cold Spring Harbor Laboratory  ·  28 Apr 2023  ·  doi:10.1101/2023.04.26.537486
bioRxiv Zymoseptoria
Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics
Divergent Outcomes of Direct Conspecific Pathogen Strain Interaction and Plant Co-Infection Suggest Consequences for Disease Dynamics
Hadjer Bellah, Nicolas F. Seiler, Daniel Croll
Microbiology Spectrum  ·  13 Apr 2023  ·  doi:10.1128/spectrum.04443-22
Zymoseptoria
Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus
Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus
Sergio M. Latorre, Vincent M. Were, Andrew J. Foster, Thorsten Langner, Angus Malmgren, …, Batiseba Tembo, Joe Win, Nicholas J. Talbot, Hernán A. Burbano, Sophien Kamoun
PLOS Biology  ·  11 Apr 2023  ·  doi:10.1371/journal.pbio.3002052
Wheat blast
A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
Alice Feurtey, Cécile Lorrain, Megan C. McDonald, Andrew Milgate, Peter S. Solomon, …, Eva H. Stukenbrock, Marc-Henri Lebrun, Gert H. J. Kema, Bruce A. McDonald, Daniel Croll
Nature Communications  ·  24 Feb 2023  ·  doi:10.1038/s41467-023-36674-y
Github
Highlight TEs Zymoseptoria
Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen
Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen
Ursula Oggenfuss, Daniel Croll
PLOS Pathogens  ·  14 Feb 2023  ·  doi:10.1371/journal.ppat.1011130
Highlight TEs Zymoseptoria
A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici
A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici
Hadjer Bellah, Gwilherm Gazeau, Sandrine Gélisse, Reda Amezrou, Thierry C. Marcel, Daniel Croll
PLOS ONE  ·  06 Feb 2023  ·  doi:10.1371/journal.pone.0281181
Zymoseptoria
Genome Evolution in Fungal Plant Pathogens: From Populations to Kingdom-Wide Dynamics
Genome Evolution in Fungal Plant Pathogens: From Populations to Kingdom-Wide Dynamics
Ursula Oggenfuss, Alice Feurtey, Claudia Sarai Reyes-Avila, Emile Gluck-Thaler, Guido Puccetti, …, Leen Nanchira Abraham, Luzia Stalder, Sabina Moser Tralamazza, Sandra Milena González-Sáyer, Daniel Croll
The Mycota  ·  01 Jan 2023  ·  doi:10.1007/978-3-031-29199-9_5
Book chapter Review

2022

Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome
Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome
Vinciane Monod, Valérie Hofstetter, Vivian Zufferey, Olivier Viret, Katia Gindro, Daniel Croll
Microbiology Spectrum  ·  21 Dec 2022  ·  doi:10.1128/spectrum.02513-22
Microbiome
Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen
Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen
Nikhil Kumar Singh, Sabina Moser Tralamazza, Leen Nanchira Abraham, Gaétan Glauser, Daniel Croll
BMC Biology  ·  08 Oct 2022  ·  doi:10.1186/s12915-022-01422-z
Zymoseptoria
Unraveling coevolutionary dynamics using ecological genomics
Unraveling coevolutionary dynamics using ecological genomics
Cornille Amandine, Dieter Ebert, Eva Stukenbrock, Ricardo C. Rodríguez de la Vega, Peter Tiffin, Daniel Croll, Aurélien Tellier
Trends in Genetics  ·  01 Oct 2022  ·  doi:10.1016/j.tig.2022.05.008
Review
Genome of Malassezia arunalokei and Its Distribution on Facial Skin
Genome of Malassezia arunalokei and Its Distribution on Facial Skin
Yong-Joon Cho, Taeyune Kim, Daniel Croll, Minji Park, Donghyeun Kim, Hye Lim Keum, Woo Jun Sul, Won Hee Jung
Microbiology Spectrum  ·  29 Jun 2022  ·  doi:10.1128/spectrum.00506-22
Human pathogens
Organic acids and glucose prime late-stage fungal biotrophy in maize
Organic acids and glucose prime late-stage fungal biotrophy in maize
Matthias Kretschmer, Djihane Damoo, Sherry Sun, Christopher W. J. Lee, Daniel Croll, Harry Brumer, James Kronstad
Science  ·  10 Jun 2022  ·  doi:10.1126/science.abo2401
Highlight Ustilago
The population genetics of adaptation through copy number variation in a fungal plant pathogen
The population genetics of adaptation through copy number variation in a fungal plant pathogen
Luzia Stalder, Ursula Oggenfuss, Norfarhan Mohd‐Assaad, Daniel Croll
Molecular Ecology  ·  05 Apr 2022  ·  doi:10.1111/mec.16435
Rhynchosprium
The era of reference genomes in conservation genomics
The era of reference genomes in conservation genomics
Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, …, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
Trends in Ecology & Evolution  ·  01 Mar 2022  ·  doi:10.1016/j.tree.2021.11.008
Review Conservation genomics
A devil's bargain with transposable elements in plant pathogens
A devil's bargain with transposable elements in plant pathogens
Simone Fouché, Ursula Oggenfuss, Emilie Chanclud, Daniel Croll
Trends in Genetics  ·  01 Mar 2022  ·  doi:10.1016/j.tig.2021.08.005
Highlight Review
Temporal changes in pathogen diversity in a perennial plant–pathogen–hyperparasite system
Temporal changes in pathogen diversity in a perennial plant–pathogen–hyperparasite system
Lea Stauber, Daniel Croll, Simone Prospero
Molecular Ecology  ·  16 Feb 2022  ·  doi:10.1111/mec.16386
Cryphonectria
Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat
Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat
Evan John, Silke Jacques, Huyen T. T. Phan, Lifang Liu, Danilo Pereira, Daniel Croll, Karam B. Singh, Richard P. Oliver, Kar-Chun Tan
PLOS Pathogens  ·  06 Jan 2022  ·  doi:10.1371/journal.ppat.1010149
Parastagonospora
High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees
High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees
Sandra González-Sayer, Ursula Oggenfuss, Ibonne García, Fabio Aristizabal, Daniel Croll, Diego M. Riaño-Pachon
Genetics and Molecular Biology  ·  01 Jan 2022  ·  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
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population
F Gözde Çilingir, Luke A’Bear, Dennis Hansen, Leyla R Davis, Nancy Bunbury, Arpat Ozgul, Daniel Croll, Christine Grossen
GigaScience  ·  01 Jan 2022  ·  doi:10.1093/gigascience/giac090
Conservation genomics

2021

Screening of grapevine red blotch virus in two European ampelographic collections
Screening of grapevine red blotch virus in two European ampelographic collections
Jean-Sébastien Reynard, Justine Brodard, Nathalie Dubuis, Isabelle Kellenberger, Anne-Sophie Spilmont, …, Daniel Croll, Katia Gindro, Olivier Schumpp, Jean-Laurent Spring, Thierry Lacombe
Journal of Plant Pathology  ·  12 Nov 2021  ·  doi:10.1007/s42161-021-00952-9
Grapevine
Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi
Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi
Sabina Moser Tralamazza, Leen Nanchira Abraham, Claudia Sarai Reyes-Avila, Benedito Corrêa, Daniel Croll
Molecular Biology and Evolution  ·  09 Nov 2021  ·  doi:10.1093/molbev/msab323
Highlight
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici
Nikhil Kumar Singh, Petteri Karisto, Daniel Croll
Microbial Genomics  ·  01 Nov 2021  ·  doi:10.1099/mgen.0.000678
Zymoseptoria
Soil composition and plant genotype determine benzoxazinoid‐mediated plant–soil feedbacks in cereals
Soil composition and plant genotype determine benzoxazinoid‐mediated plant–soil feedbacks in cereals
Selma Cadot, Valentin Gfeller, Lingfei Hu, Nikhil Singh, Andrea Sánchez‐Vallet, Gaétan Glauser, Daniel Croll, Matthias Erb, Marcel G. A. van der Heijden, Klaus Schlaeppi
Plant, Cell & Environment  ·  23 Sep 2021  ·  doi:10.1111/pce.14184
Zymoseptoria
A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
Ursula Oggenfuss, Thomas Badet, Thomas Wicker, Fanny E Hartmann, Nikhil Kumar Singh, …, Petteri Karisto, Tiziana Vonlanthen, Christopher Mundt, Bruce A McDonald, Daniel Croll
eLife  ·  16 Sep 2021  ·  doi:10.7554/eLife.69249
Highlight TEs Zymoseptoria
Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus <scp><i>Cenococcum geophilum</i></scp>
Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum
Benjamin Dauphin, Maíra de Freitas Pereira, Annegret Kohler, Igor V. Grigoriev, Kerrie Barry, …, Mojgan Amirebrahimi, Anna Lipzen, Francis Martin, Martina Peter, Daniel Croll
Environmental Microbiology  ·  15 Sep 2021  ·  doi:10.1111/1462-2920.15752
Mycorrhizal fungi
Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen
Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen
Danilo Pereira, Ursula Oggenfuss, Bruce A. McDonald, Daniel Croll
Microbial Genomics  ·  31 Aug 2021  ·  doi:10.1099/mgen.0.000540
Parastagonospora TEs
Transcriptome‐wide SNPs for <i>Botrychium lunaria</i> ferns enable fine‐grained analysis of ploidy and population structure
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure
Vinciane Mossion, Benjamin Dauphin, Jason Grant, Michael Kessler, Niklaus Zemp, Daniel Croll
Molecular Ecology Resources  ·  07 Aug 2021  ·  doi:10.1111/1755-0998.13478
Ferns
A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics
A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics
Camille Kessler, Alice Brambilla, Dominique Waldvogel, Glauco Camenisch, Iris Biebach, Deborah M. Leigh, Christine Grossen, Daniel Croll
Molecular Ecology Resources  ·  07 Jul 2021  ·  doi:10.1111/1755-0998.13452
Conservation genomics
Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen
Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen
Thomas Badet, Simone Fouché, Fanny E. Hartmann, Marcello Zala, Daniel Croll
Nature Communications  ·  10 Jun 2021  ·  doi:10.1038/s41467-021-23862-x
Github
Highlight Zymoseptoria
A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire
A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire
Alba Hendier, Cyrille Chatelain, Pierre‐Emmanuel Du Pasquier, Monique Paris, Karim Ouattara, Inza Koné, Daniel Croll, Klaus Zuberbühler
African Journal of Ecology  ·  09 Jun 2021  ·  doi:10.1111/aje.12888
Conservation
Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
Nikhil Kumar Singh, Thomas Badet, Leen Abraham, Daniel Croll
BMC Genomics  ·  27 May 2021  ·  doi:10.1186/s12864-021-07691-2
Zymoseptoria
Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection
Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection
Anik Dutta, Daniel Croll, Bruce A. McDonald, Simon G. Krattinger
Euphytica  ·  11 May 2021  ·  doi:10.1007/s10681-021-02843-7
Zymoseptoria
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
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
Daniel Croll
Zenodo  ·  01 Apr 2021  ·  doi:10.5281/zenodo.4655959
Zenodo
Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
Lea Stauber, Thomas Badet, Alice Feurtey, Simone Prospero, Daniel Croll
eLife  ·  05 Mar 2021  ·  doi:10.7554/eLife.56279
Highlight Cryphonectria
Fusarium: more than a node or a foot-shaped basal cell
Fusarium: more than a node or a foot-shaped basal cell
P.W. Crous, L. Lombard, M. Sandoval-Denis, K.A. Seifert, H.-J. Schroers, …, A. Yurkov, J.C. Zamora, R. Zare, C.L. Zhang, M. Thines
Studies in Mycology  ·  01 Mar 2021  ·  doi:10.1016/j.simyco.2021.100116
Fusarium
Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
Anik Dutta, Fanny E Hartmann, Carolina Sardinha Francisco, Bruce A McDonald, Daniel Croll
The ISME Journal  ·  15 Jan 2021  ·  doi:10.1038/s41396-020-00859-w
Highlight Zymoseptoria
Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses
Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses
D. Croll, P.W. Crous, D. Pereira, E.A. Mordecai, B.A. McDonald, P.C. Brunner
Persoonia - Molecular Phylogeny and Evolution of Fungi  ·  01 Jan 2021  ·  doi:10.3767/persoonia.2021.46.04
Parastagonospora
Chapter 10. Omics-based Detection, Identification and Quantification of GM Food and Feed: Current Challenges and Perspectives
Chapter 10. Omics-based Detection, Identification and Quantification of GM Food and Feed: Current Challenges and Perspectives
Sylvain Aubry, Sarai Reyes Avila, Daniel Croll, Bastien Christ
Food Chemistry, Function and Analysis  ·  01 Jan 2021  ·  doi:10.1039/9781839163005-00257
Book chapter Review
Tackling microbial threats in agriculture with integrative imaging and computational approaches
Tackling microbial threats in agriculture with integrative imaging and computational approaches
Nikhil Kumar Singh, Anik Dutta, Guido Puccetti, Daniel Croll
Computational and Structural Biotechnology Journal  ·  01 Jan 2021  ·  doi:10.1016/j.csbj.2020.12.018
Review
Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation
Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation
Cécile Lorrain, Ursula Oggenfuss, Daniel Croll, Sebastien Duplessis, Eva Stukenbrock
Encyclopedia of Mycology  ·  01 Jan 2021  ·  doi:10.1016/B978-0-12-819990-9.00042-1
Book chapter Review TEs

2020

The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen
The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen
Fanny E. Hartmann, Tiziana Vonlanthen, Nikhil Kumar Singh, Megan C. McDonald, Andrew Milgate, Daniel Croll
Molecular Ecology  ·  12 Dec 2020  ·  doi:10.1111/mec.15737
Zymoseptoria
Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus<i>Cryphonectria</i>
Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the GenusCryphonectria
Lea Stauber, Simone Prospero, Daniel Croll
mSphere  ·  28 Oct 2020  ·  doi:10.1128/mSphere.00737-20
Cryphonectria
A Chromosome-Scale Genome Assembly for the <i>Fusarium oxysporum</i> Strain Fo5176 To Establish a Model <i>Arabidopsis</i>-Fungal Pathosystem
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem
Like Fokkens, Li Guo, Susanne Dora, Bo Wang, Kai Ye, Clara Sánchez-Rodríguez, Daniel Croll
G3 Genes|Genomes|Genetics  ·  01 Oct 2020  ·  doi:10.1534/g3.120.401375
Fusarium
The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen
The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen
Danilo Pereira, Bruce A McDonald, Daniel Croll
Genome Biology and Evolution  ·  28 Sep 2020  ·  doi:10.1093/gbe/evaa203
Parastagonospora
Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen
Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen
Anik Dutta, Daniel Croll, Bruce A. McDonald, Luke G. Barrett
Evolutionary Applications  ·  24 Sep 2020  ·  doi:10.1111/eva.13117
Zymoseptoria
Transcriptome plasticity underlying plant root colonization and insect invasion by <i>Pseudomonas protegens</i>
Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
Pilar Vesga, Pascale Flury, Jordan Vacheron, Christoph Keel, Daniel Croll, Monika Maurhofer
The ISME Journal  ·  02 Sep 2020  ·  doi:10.1038/s41396-020-0729-9
Microbiome
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model
David E. Torres, Ursula Oggenfuss, Daniel Croll, Michael F. Seidl
Fungal Biology Reviews  ·  01 Sep 2020  ·  doi:10.1016/j.fbr.2020.07.001
Review TEs
Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus, Eva H. Stukenbrock
BMC Genomics  ·  26 Aug 2020  ·  doi:10.1186/s12864-020-06871-w
Zymoseptoria
The rise and fall of genes: origins and functions of plant pathogen pangenomes
The rise and fall of genes: origins and functions of plant pathogen pangenomes
Thomas Badet, Daniel Croll
Current Opinion in Plant Biology  ·  01 Aug 2020  ·  doi:10.1016/j.pbi.2020.04.009
Highlight Review
Natural selection drives population divergence for local adaptation in a wheat pathogen
Natural selection drives population divergence for local adaptation in a wheat pathogen
Danilo Pereira, Daniel Croll, Patrick C. Brunner, Bruce A. McDonald
Fungal Genetics and Biology  ·  01 Aug 2020  ·  doi:10.1016/j.fgb.2020.103398
Parastagonospora
A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
Andrea Sánchez-Vallet, Hui Tian, Luis Rodriguez-Moreno, Dirk-Jan Valkenburg, Raspudin Saleem-Batcha, …, H. Peter van Esse, Alga Zuccaro, Daniel Croll, Jeroen R. Mesters, Bart P. H. J. Thomma
PLOS Pathogens  ·  23 Jun 2020  ·  doi:10.1371/journal.ppat.1008652
Zymoseptoria
Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae
Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae
Renate Heinzelmann, Daniel Rigling, György Sipos, Martin Münsterkötter, Daniel Croll
Heredity  ·  13 Mar 2020  ·  doi:10.1038/s41437-020-0306-z
Armillaria
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
Christine Grossen, Frédéric Guillaume, Lukas F. Keller, Daniel Croll
Nature Communications  ·  21 Feb 2020  ·  doi:10.1038/s41467-020-14803-1
Highlight Conservation genomics
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
Thomas Badet, Ursula Oggenfuss, Leen Abraham, Bruce A. McDonald, Daniel Croll
BMC Biology  ·  11 Feb 2020  ·  doi:10.1186/s12915-020-0744-3
Zymoseptoria

2019

Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex
Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex
Sabina Moser Tralamazza, Liliana Oliveira Rocha, Ursula Oggenfuss, Benedito Corrêa, Daniel Croll
Genome Biology and Evolution  ·  14 Oct 2019  ·  doi:10.1093/gbe/evz225
Fusarium
Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen
Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen
Simone Fouché, Thomas Badet, Ursula Oggenfuss, Clémence Plissonneau, Carolina Sardinha Francisco, Daniel Croll
Molecular Biology and Evolution  ·  23 Sep 2019  ·  doi:10.1093/molbev/msz216
Highlight TEs Zymoseptoria
The emergence of the multi‐species NIP1 effector in <i>Rhynchosporium</i> was accompanied by high rates of gene duplications and losses
The emergence of the multi‐species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
Norfarhan Mohd‐Assaad, Bruce A. McDonald, Daniel Croll
Environmental Microbiology  ·  11 Apr 2019  ·  doi:10.1111/1462-2920.14583
Rhynchosporium
Cautionary Notes on Use of the MoT3 Diagnostic Assay for <i>Magnaporthe oryzae</i> Wheat and Rice Blast Isolates
Cautionary Notes on Use of the MoT3 Diagnostic Assay for Magnaporthe oryzae Wheat and Rice Blast Isolates
Dipali Rani Gupta, Claudia Sarai Reyes Avila, Joe Win, Darren M. Soanes, Lauren S. Ryder, …, Musrat Zahan Surovy, Md. Mahbubur Rahman, Nicholas J. Talbot, Sophien Kamoun, M. Tofazzal Islam
Phytopathology®  ·  01 Apr 2019  ·  doi:10.1094/PHYTO-06-18-0199-LE
Wheat blast
Rapid Parallel Evolution of Azole Fungicide Resistance in Australian Populations of the Wheat Pathogen <i>Zymoseptoria tritici</i>
Rapid Parallel Evolution of Azole Fungicide Resistance in Australian Populations of the Wheat Pathogen Zymoseptoria tritici
Megan C. McDonald, Melanie Renkin, Merrin Spackman, Beverley Orchard, Daniel Croll, Peter S. Solomon, Andrew Milgate
Applied and Environmental Microbiology  ·  15 Feb 2019  ·  doi:10.1128/AEM.01908-18
Zymoseptoria

2018

The Monothiol Glutaredoxin Grx4 Regulates Iron Homeostasis and Virulence in Cryptococcus neoformans
The Monothiol Glutaredoxin Grx4 Regulates Iron Homeostasis and Virulence in Cryptococcus neoformans
Rodgoun Attarian, Guanggan Hu, Eddy Sánchez-León, Mélissa Caza, Daniel Croll, …, Horacio Bach, Tricia Missall, Jennifer Lodge, Won Hee Jung, James W. Kronstad
mBio  ·  21 Dec 2018  ·  doi:10.1128/mBio.02377-18
Human pathogens
The birth and death of effectors in rapidly evolving filamentous pathogen genomes
The birth and death of effectors in rapidly evolving filamentous pathogen genomes
Simone Fouché, Clémence Plissonneau, Daniel Croll
Current Opinion in Microbiology  ·  01 Dec 2018  ·  doi:10.1016/j.mib.2018.01.020
Review Highlight
Wheat blast: from its origins in South America to its emergence as a global threat
Wheat blast: from its origins in South America to its emergence as a global threat
Paulo Cezar Ceresini, Vanina Lilián Castroagudín, Fabrício Ávila Rodrigues, Jonas Alberto Rios, Carlos Eduardo Aucique‐Pérez, …, Daniel Croll, Eduardo Alves, Giselle de Carvalho, João Leodato Nunes Maciel, Bruce Alan McDonald
Molecular Plant Pathology  ·  24 Oct 2018  ·  doi:10.1111/mpp.12747
Review Wheat blast
The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
Andrea Sánchez-Vallet, Simone Fouché, Isabelle Fudal, Fanny E. Hartmann, Jessica L. Soyer, Aurélien Tellier, Daniel Croll
Annual Review of Phytopathology  ·  25 Aug 2018  ·  doi:10.1146/annurev-phyto-080516-035303
Highlight Review
Wheat Blast: Past, Present, and Future
Wheat Blast: Past, Present, and Future
Paulo Cezar Ceresini, Vanina Lilián Castroagudín, Fabrício Ávila Rodrigues, Jonas Alberto Rios, Carlos Eduardo Aucique-Pérez, Silvino Intra Moreira, Eduardo Alves, Daniel Croll, João Leodato Nunes Maciel
Annual Review of Phytopathology  ·  25 Aug 2018  ·  doi:10.1146/annurev-phyto-080417-050036
Review Wheat blast
Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat
Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat
Parvathy Krishnan, Lukas Meile, Clémence Plissonneau, Xin Ma, Fanny E. Hartmann, Daniel Croll, Bruce A. McDonald, Andrea Sánchez-Vallet
BMC Biology  ·  16 Jul 2018  ·  doi:10.1186/s12915-018-0543-2
Zymoseptoria
Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici
Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici
Simone Fouché, Clémence Plissonneau, Bruce A McDonald, Daniel Croll
Genome Biology and Evolution  ·  29 May 2018  ·  doi:10.1093/gbe/evy100
Zymoseptoria
Genome‐wide evidence for divergent selection between populations of a major agricultural pathogen
Genome‐wide evidence for divergent selection between populations of a major agricultural pathogen
Fanny E. Hartmann, Bruce A. McDonald, Daniel Croll
Molecular Ecology  ·  23 May 2018  ·  doi:10.1111/mec.14711
Zymoseptoria
Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen
Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen
Norfarhan Mohd-Assaad, Bruce A McDonald, Daniel Croll
Genome Biology and Evolution  ·  01 May 2018  ·  doi:10.1093/gbe/evy087
Rhynchosporium
Genomewide signatures of selection in <i>Epichloë</i> reveal candidate genes for host specialization
Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization
Melanie K. Schirrmann, Stefan Zoller, Daniel Croll, Eva H. Stukenbrock, Adrian Leuchtmann, Simone Fior
Molecular Ecology  ·  27 Apr 2018  ·  doi:10.1111/mec.14585
Epichloë
A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
Lukas Meile, Daniel Croll, Patrick C. Brunner, Clémence Plissonneau, Fanny E. Hartmann, Bruce A. McDonald, Andrea Sánchez‐Vallet
New Phytologist  ·  25 Apr 2018  ·  doi:10.1111/nph.15180
Zymoseptoria
Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization
Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization
Juliana Benevenuto, Natalia S. Teixeira-Silva, Eiko E. Kuramae, Daniel Croll, Claudia B. Monteiro-Vitorello
Frontiers in Microbiology  ·  06 Apr 2018  ·  doi:10.3389/fmicb.2018.00660
Ustilago
Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome
Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome
Clémence Plissonneau, Fanny E. Hartmann, Daniel Croll
BMC Biology  ·  11 Jan 2018  ·  doi:10.1186/s12915-017-0457-4
Zymoseptoria
Acetate provokes mitochondrial stress and cell death in <i>Ustilago maydis</i>
Acetate provokes mitochondrial stress and cell death in Ustilago maydis
Matthias Kretschmer, Scott Lambie, Daniel Croll, James W. Kronstad
Molecular Microbiology  ·  03 Jan 2018  ·  doi:10.1111/mmi.13894
Ustilago

2017

Nature's genetic screens: using genome‐wide association studies for effector discovery
Nature's genetic screens: using genome‐wide association studies for effector discovery
Andrea Sánchez‐Vallet, Fanny E. Hartmann, Thierry C. Marcel, Daniel Croll
Molecular Plant Pathology  ·  11 Dec 2017  ·  doi:10.1111/mpp.12592
Review
High-density genetic mapping identifies the genetic basis of a natural colony morphology mutant in the root rot pathogen Armillaria ostoyae
High-density genetic mapping identifies the genetic basis of a natural colony morphology mutant in the root rot pathogen Armillaria ostoyae
Renate Heinzelmann, Daniel Croll, Stefan Zoller, György Sipos, Martin Münsterkötter, Ulrich Güldener, Daniel Rigling
Fungal Genetics and Biology  ·  01 Nov 2017  ·  doi:10.1016/j.fgb.2017.08.007
Armillaria
Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations
Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations
Christine Grossen, Iris Biebach, Samer Angelone‐Alasaad, Lukas F. Keller, Daniel Croll
Evolutionary Applications  ·  27 Oct 2017  ·  doi:10.1111/eva.12490
Conservation genomics
The wheat blast pathogen<i>Pyricularia graminis-tritici</i>has complex origins and a disease cycle spanning multiple grass hosts
The wheat blast pathogenPyricularia graminis-triticihas complex origins and a disease cycle spanning multiple grass hosts
Vanina L. Castroagudín, Anderson L. D. Danelli, Silvino I. Moreira, Juliana T. A. Reges, Giselle de Carvalho, …, Carlos A. Forcelini, Eduardo Alves, Bruce A. McDonald, Daniel Croll, Paulo C. Ceresini
Cold Spring Harbor Laboratory  ·  16 Oct 2017  ·  doi:10.1101/203455
bioRxiv
Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen
Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen
Fanny E. Hartmann, Daniel Croll
Molecular Biology and Evolution  ·  21 Jul 2017  ·  doi:10.1093/molbev/msx208
Highlight Zymoseptoria
Comparative Transcriptome Analyses in<i>Zymoseptoria tritici</i>Reveal Significant Differences in Gene Expression Among Strains During Plant Infection
Comparative Transcriptome Analyses inZymoseptoria triticiReveal Significant Differences in Gene Expression Among Strains During Plant Infection
Javier Palma-Guerrero, Xin Ma, Stefano F. F. Torriani, Marcello Zala, Carolina S. Francisco, Fanny E. Hartmann, Daniel Croll, Bruce A. McDonald
Molecular Plant-Microbe Interactions®  ·  01 Mar 2017  ·  doi:10.1094/MPMI-07-16-0146-R
Zymoseptoria
Can Evolution Supply What Ecology Demands?
Can Evolution Supply What Ecology Demands?
Hanna Kokko, Anurag Chaturvedi, Daniel Croll, Martin C. Fischer, Frédéric Guillaume, Sophie Karrenberg, Ben Kerr, Gregor Rolshausen, Jessica Stapley
Trends in Ecology & Evolution  ·  01 Mar 2017  ·  doi:10.1016/j.tree.2016.12.005
A small secreted protein in <i>Zymoseptoria tritici</i> is responsible for avirulence on wheat cultivars carrying the <i>Stb6</i> resistance gene
A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene
Ziming Zhong, Thierry C. Marcel, Fanny E. Hartmann, Xin Ma, Clémence Plissonneau, …, Nicolas Lapalu, Joëlle Amselem, Bruce A. McDonald, Daniel Croll, Javier Palma‐Guerrero
New Phytologist  ·  06 Feb 2017  ·  doi:10.1111/nph.14434
Zymoseptoria
Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen<i>Zymoseptoria tritici</i>
Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogenZymoseptoria tritici
Ethan l. Stewart, Daniel Croll, Mark H. Lendenmann, Andrea Sanchez‐Vallet, Fanny E. Hartmann, Javier Palma‐Guerrero, Xin Ma, Bruce A. McDonald
Molecular Plant Pathology  ·  05 Feb 2017  ·  doi:10.1111/mpp.12515
Zymoseptoria
Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution
Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution
Clémence Plissonneau, Juliana Benevenuto, Norfarhan Mohd-Assaad, Simone Fouché, Fanny E. Hartmann, Daniel Croll
Frontiers in Plant Science  ·  03 Feb 2017  ·  doi:10.3389/fpls.2017.00119
Review
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
Fanny E Hartmann, Andrea Sánchez-Vallet, Bruce A McDonald, Daniel Croll
The ISME Journal  ·  24 Jan 2017  ·  doi:10.1038/ismej.2016.196
Highlight Zymoseptoria

2016

Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations
Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations
Norfarhan Mohd‐Assaad, Bruce A. McDonald, Daniel Croll
Molecular Ecology  ·  30 Nov 2016  ·  doi:10.1111/mec.13916
Rhychosporium
Maize susceptibility to <i>Ustilago maydis</i> is influenced by genetic and chemical perturbation of carbohydrate allocation
Maize susceptibility to Ustilago maydis is influenced by genetic and chemical perturbation of carbohydrate allocation
Matthias Kretschmer, Daniel Croll, James W. Kronstad
Molecular Plant Pathology  ·  14 Nov 2016  ·  doi:10.1111/mpp.12486
Ustilago
Chloroplast‐associated metabolic functions influence the susceptibility of maize to <i>Ustilago maydis</i>
Chloroplast‐associated metabolic functions influence the susceptibility of maize to Ustilago maydis
Matthias Kretschmer, Daniel Croll, James W. Kronstad
Molecular Plant Pathology  ·  14 Nov 2016  ·  doi:10.1111/mpp.12485
Ustilago
The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat
The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat
Clémence Plissonneau, Alessandra Stürchler, Daniel Croll
mBio  ·  02 Nov 2016  ·  doi:10.1128/mBio.01231-16
Zymoseptoria
The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems
The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems
Daniel Croll, Bruce A. McDonald
Molecular Ecology  ·  24 Oct 2016  ·  doi:10.1111/mec.13870
Zymoseptoria
What the population genetic structures of host and pathogen tell us about disease evolution
What the population genetic structures of host and pathogen tell us about disease evolution
Daniel Croll, Anna‐Liisa Laine
New Phytologist  ·  13 Oct 2016  ·  doi:10.1111/nph.14203
Review
Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
M. Tofazzal Islam, Daniel Croll, Pierre Gladieux, Darren M. Soanes, Antoine Persoons, …, Daniel Swan, Nicholas J. Talbot, Diane G. O. Saunders, Joe Win, Sophien Kamoun
BMC Biology  ·  03 Oct 2016  ·  doi:10.1186/s12915-016-0309-7
Wheat blast
Evolution in the absence of sex: Ideas revisited in the post‐genomics age (retrospective on DOI 10.1002/bies.201300155)
Evolution in the absence of sex: Ideas revisited in the post‐genomics age (retrospective on DOI 10.1002/bies.201300155)
Daniel Croll
BioEssays  ·  19 Sep 2016  ·  doi:10.1002/bies.201600195
Review
Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact
Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact
Christine Grossen, Sampath S. Seneviratne, Daniel Croll, Darren E. Irwin
Molecular Ecology  ·  26 Aug 2016  ·  doi:10.1111/mec.13751
The putative phospholipase Lip2 counteracts oxidative damage and influences the virulence of <i>Ustilago maydis</i>
The putative phospholipase Lip2 counteracts oxidative damage and influences the virulence of Ustilago maydis
Scott C. Lambie, Matthias Kretschmer, Daniel Croll, Tegan M. Haslam, Ljerka Kunst, Jana Klose, James W. Kronstad
Molecular Plant Pathology  ·  21 Apr 2016  ·  doi:10.1111/mpp.12391
Ustilago
Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation
Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation
J. M. H. Geddes, M. Caza, D. Croll, N. Stoynov, L. J. Foster, J. W. Kronstad
mBio  ·  02 Mar 2016  ·  doi:10.1128/mBio.01862-15
Human pathogens
Comparative transcriptomic analyses of <scp><i>Z</i></scp><i>ymoseptoria tritici</i> strains show complex lifestyle transitions and intraspecific variability in transcription profiles
Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles
Javier Palma‐Guerrero, Stefano F. F. Torriani, Marcello Zala, Dee Carter, Mikaël Courbot, Jason J. Rudd, Bruce A. McDonald, Daniel Croll
Molecular Plant Pathology  ·  08 Feb 2016  ·  doi:10.1111/mpp.12333
Zymoseptoria
QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici
QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici
M H Lendenmann, D Croll, J Palma-Guerrero, E L Stewart, B A McDonald
Heredity  ·  13 Jan 2016  ·  doi:10.1038/hdy.2015.111
Zymoseptoria

2015

Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A
Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A
Jennifer M. H. Geddes, Daniel Croll, Mélissa Caza, Nikolay Stoynov, Leonard J. Foster, James W. Kronstad
BMC Microbiology  ·  09 Oct 2015  ·  doi:10.1186/s12866-015-0532-3
Human pathogens
The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen
The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen
Daniel Croll, Mark H Lendenmann, Ethan Stewart, Bruce A McDonald
Genetics  ·  21 Sep 2015  ·  doi:10.1534/genetics.115.180968
Zymoseptoria
QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici
QTL mapping of fungicide sensitivity reveals novel genes and pleiotropy with melanization in the pathogen Zymoseptoria tritici
Mark H. Lendenmann, Daniel Croll, Bruce A. McDonald
Fungal Genetics and Biology  ·  01 Jul 2015  ·  doi:10.1016/j.fgb.2015.05.001
Zymoseptoria
Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis
Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis
Won Hee Jung, Daniel Croll, Jae Hoon Cho, Yu Ri Kim, Yang Won Lee
Mycoses  ·  10 Feb 2015  ·  doi:10.1111/myc.12296
Human pathogen

2014

Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus<i>Zymoseptoria tritici</i>
Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic FungusZymoseptoria tritici
Mark H Lendenmann, Daniel Croll, Ethan L Stewart, Bruce A McDonald
G3 Genes|Genomes|Genetics  ·  01 Dec 2014  ·  doi:10.1534/g3.114.015289
Zymoseptoria
Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution
Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution
R. Blake Billmyre, Daniel Croll, Wenjun Li, Piotr Mieczkowski, Dee A. Carter, Christina A. Cuomo, James W. Kronstad, Joseph Heitman
mBio  ·  29 Aug 2014  ·  doi:10.1128/mBio.01494-14
Human pathogens
Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
Christine Grossen, Lukas Keller, Iris Biebach, Daniel Croll
PLoS Genetics  ·  19 Jun 2014  ·  doi:10.1371/journal.pgen.1004438
Conservation genomics
The evolving fungal genome
The evolving fungal genome
Eva H. Stukenbrock, Daniel Croll
Fungal Biology Reviews  ·  01 May 2014  ·  doi:10.1016/j.fbr.2014.02.001
Review
Hitchhiking Selection Is Driving Intron Gain in a Pathogenic Fungus
Hitchhiking Selection Is Driving Intron Gain in a Pathogenic Fungus
Patrick C. Brunner, Stefano F.F. Torriani, Daniel Croll, Eva H. Stukenbrock, Bruce A. McDonald
Molecular Biology and Evolution  ·  07 Apr 2014  ·  doi:10.1093/molbev/msu123
Zymoseptoria
Learn from the fungi: Adaptive evolution without sex in fungal pathogens (comment on DOI 10.1002/bies.201300155)
Learn from the fungi: Adaptive evolution without sex in fungal pathogens (comment on DOI 10.1002/bies.201300155)
Daniel Croll
BioEssays  ·  05 Mar 2014  ·  doi:10.1002/bies.201400030
Review

2013

An assay for quantitative virulence in <i><scp>R</scp>hynchosporium commune</i> reveals an association between effector genotype and virulence
An assay for quantitative virulence in Rhynchosporium commune reveals an association between effector genotype and virulence
T. S. Stefansson, Y. Willi, D. Croll, B. A. McDonald
Plant Pathology  ·  06 Aug 2013  ·  doi:10.1111/ppa.12111
Rhynchosporium
Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen
Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen
Daniel Croll, Marcello Zala, Bruce A. McDonald
PLoS Genetics  ·  13 Jun 2013  ·  doi:10.1371/journal.pgen.1003567
Highlight Zymoseptoria
Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen
Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen
Patrick C. Brunner, Stefano F.F. Torriani, Daniel Croll, Eva H. Stukenbrock, Bruce A. McDonald
Molecular Biology and Evolution  ·  20 Mar 2013  ·  doi:10.1093/molbev/mst041
Zymoseptoria

2012

Population genetic structure of Mycosphaerella graminicola and Quinone Outside Inhibitor (QoI) resistance in the Czech Republic
Population genetic structure of Mycosphaerella graminicola and Quinone Outside Inhibitor (QoI) resistance in the Czech Republic
Jana Drabešová, Pavel Ryšánek, Patrick Brunner, Bruce A. McDonald, Daniel Croll
European Journal of Plant Pathology  ·  14 Sep 2012  ·  doi:10.1007/s10658-012-0080-8
Zymoseptoria
The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens
The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens
Daniel Croll, Bruce A. McDonald
PLoS Pathogens  ·  26 Apr 2012  ·  doi:10.1371/journal.ppat.1002608
Highlight Review
What if esca disease of grapevine were not a fungal disease?
What if esca disease of grapevine were not a fungal disease?
Valérie Hofstetter, Bart Buyck, Daniel Croll, Olivier Viret, Arnaud Couloux, Katia Gindro
Fungal Diversity  ·  24 Apr 2012  ·  doi:10.1007/s13225-012-0171-z
Microbiome
Intron Gains and Losses in the Evolution of Fusarium and Cryptococcus Fungi
Intron Gains and Losses in the Evolution of Fusarium and Cryptococcus Fungi
Daniel Croll, Bruce A. McDonald
Genome Biology and Evolution  ·  01 Jan 2012  ·  doi:10.1093/gbe/evs091

2011

Evidence for Extensive Recent Intron Transposition in Closely Related Fungi
Evidence for Extensive Recent Intron Transposition in Closely Related Fungi
Stefano F.F. Torriani, Eva H. Stukenbrock, Patrick C. Brunner, Bruce A. McDonald, Daniel Croll
Current Biology  ·  01 Dec 2011  ·  doi:10.1016/j.cub.2011.10.041
Highlight Zymoseptoria
The transcriptome of the arbuscular mycorrhizal fungus <i>Glomus intraradices</i> (DAOM 197198) reveals functional tradeoffs in an obligate symbiont
The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont
E. Tisserant, A. Kohler, P. Dozolme‐Seddas, R. Balestrini, K. Benabdellah, …, Y. Shachar‐Hill, G. Tuskan, J. P. W. Young, V. Gianinazzi‐Pearson, F. Martin
New Phytologist  ·  16 Nov 2011  ·  doi:10.1111/j.1469-8137.2011.03948.x
Mycorrhizal fungi
A cryptic heterogametic transition revealed by sex‐linked DNA markers in Palearctic green toads
A cryptic heterogametic transition revealed by sex‐linked DNA markers in Palearctic green toads
M. STÖCK, D. CROLL, Z. DUMAS, S. BIOLLAY, J. WANG, N. PERRIN
Journal of Evolutionary Biology  ·  21 Feb 2011  ·  doi:10.1111/j.1420-9101.2011.02239.x
Frogs

2010

Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner
Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner
Ian R. Sanders, Daniel Croll
Annual Review of Genetics  ·  01 Dec 2010  ·  doi:10.1146/annurev-genet-102108-134239
Review Mycorrhizal fungi
Segregation in a Mycorrhizal Fungus Alters Rice Growth and Symbiosis-Specific Gene Transcription
Segregation in a Mycorrhizal Fungus Alters Rice Growth and Symbiosis-Specific Gene Transcription
Caroline Angelard, Alexandre Colard, Hélène Niculita-Hirzel, Daniel Croll, Ian R. Sanders
Current Biology  ·  01 Jul 2010  ·  doi:10.1016/j.cub.2010.05.031
Mycorrhizal fungi

2009

High-Level Molecular Diversity of Copper-Zinc Superoxide Dismutase Genes among and within Species of Arbuscular Mycorrhizal Fungi
High-Level Molecular Diversity of Copper-Zinc Superoxide Dismutase Genes among and within Species of Arbuscular Mycorrhizal Fungi
Nicolas Corradi, Beat Ruffner, Daniel Croll, Alexandre Colard, Ales Horák, Ian R. Sanders
Applied and Environmental Microbiology  ·  01 Apr 2009  ·  doi:10.1128/AEM.01974-08
Mycorrhizal fungi
Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus
Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus
Daniel Croll, Ian R Sanders
BMC Evolutionary Biology  ·  01 Jan 2009  ·  doi:10.1186/1471-2148-9-13
Mycorrhizal fungi

2008

Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus <i>Glomus intraradices</i>
Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus Glomus intraradices
Daniel Croll, Manuela Giovannetti, Alexander M. Koch, Cristiana Sbrana, Martine Ehinger, Peter J. Lammers, Ian R. Sanders
New Phytologist  ·  24 Dec 2008  ·  doi:10.1111/j.1469-8137.2008.02726.x
Mycorrhizal fungi
Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics
Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics
Daniel Croll, Nicolas Corradi, Hannes A. Gamper, Ian R. Sanders
New Phytologist  ·  15 Oct 2008  ·  doi:10.1111/j.1469-8137.2008.02602.x
Mycorrhizal fungi
Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus <i>Glomus intraradices</i>
Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices
Daniel Croll, Lukas Wille, Hannes A. Gamper, Natarajan Mathimaran, Peter J. Lammers, Nicolas Corradi, Ian R. Sanders
New Phytologist  ·  20 Feb 2008  ·  doi:10.1111/j.1469-8137.2008.02381.x
Mycorrhizal fungi

2007

Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population
Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population
Nicolas Corradi, Daniel Croll, Alexandre Colard, Gerrit Kuhn, Martine Ehinger, Ian R. Sanders
Applied and Environmental Microbiology  ·  01 Jan 2007  ·  doi:10.1128/AEM.01574-06
Mycorrhizal fungi

2005

Genetic variability in a population of arbuscular mycorrhizal fungi causes variation in plant growth
Genetic variability in a population of arbuscular mycorrhizal fungi causes variation in plant growth
Alexander M. Koch, Daniel Croll, Ian R. Sanders
Ecology Letters  ·  22 Nov 2005  ·  doi:10.1111/j.1461-0248.2005.00853.x
Mycorrhizal fungi