Daniel Croll
Neuchâtel
We want to understand how pathogens adapt and cause diseases. Professor of Evolutionary Genetics @UniNeuchatel. Hobbies: 👧🏻👧🏼🏔️
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Articles by Daniel Croll
Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen
Article metrics loading... /content/journal/mgen/10.1099/mgen.0.001769 Metrics Download as PowerPoint /deliver/fulltext/mgen/12/6/mgen001769.html?itemId=/content/journal/mgen/10.1099/mgen.0.001769&mimeType=html&fmt=ahah References Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M. Regulatory variation within and between species. Annu Rev Genomics Hum Genet 2011; 12:327–346 [View Article] [PubMed] [Google Scholar] Boocock J, Alexander N, Tapia LA, Walter-McNeill L, Munugala C et al.
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
Abstract Transposable elements (TEs) shape host-pathogen interactions and contribute to antimicrobial resistance, but how adaptive TEs arise in populations and how historical contingencies affect TE dynamics remains unclear. Fungal crop pathogens provide unique frameworks to address such questions due to spatially explicit sampling and well-characterized niches.
Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom
Loading metrics Open Access Peer-reviewed Research Article ? This is an uncorrected proof. Citation: Badet T, Croll D (2025) Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom. PLoS Biol 23(10): e3003433. https://doi.org/10.1371/journal.pbio.3003433 Academic Editor: Erin S. Kelleher, University of Houston, UNITED STATES OF AMERICA Received: July 22, 2025; Accepted: September 23, 2025; Published: October 15, 2025 Copyright: © 2025 Badet, Croll.
Genetic variation among progeny shapes symbiosis in a basidiomycete with poplar
Introduction Ectomycorrhizal (ECM) fungi serve as crucial mutualistic partners within temperate and certain tropical forest ecosystems, facilitating the provision of water and nutrients to the host trees (van der Heijden et al., 2015; Tedersoo et al., 2020). Given the frequent nutrient limitations in forest soils that impede plant growth, most forest tree species depend on ECM-fungal symbiosis for their nutritional needs. Consequently, c.
Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages
Abstract Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs).
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen
Abstract Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies affect TE dynamics remains unknown. Fungal pathogens in agriculture provide unique frameworks to address such questions due to the availability of spatially explicit sampling and well-characterized niche conditions.
A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom
Abstract Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Genomic defenses have evolved to counteract TE proliferation through silencing mechanisms operating at the epigenetic or transcript level. In fungi, repeat-induced point mutation (RIP) targets TEs by recognizing repetitive sequences and inducing mutagenesis.
High-resolution Profiling of Bacterial and Fungal Communities using Pangenome-Informed Taxon-Specific Long-Read Amplicons
Abstract High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Here, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons.
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific amplicons and long-read sequencing
Abstract High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. In this study, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific amplicons using PacBio circular consensus sequencing.
Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing - Nature Communications
Abstract Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions.
Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations
1 INTRODUCTION Identifying adaptive traits, elucidating their genetic basis and understanding the forces driving divergence of populations and species lie at the core of evolutionary biology research. Host–pathogen interactions are fascinating biological models to study adaptation over short evolutionary timescales because pathogens are entangled in tight biotic interactions with their hosts driving rapid coevolution (Kurtz et al., 2016; Paterson et al., 2010).
Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen
Loading metrics Open Access Peer-reviewed Research Article ? This is an uncorrected proof. Citation: Dutta A, McDonald BA, Croll D (2023) Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen. PLoS Pathog 19(11): e1011801. https://doi.org/10.1371/journal.ppat.1011801 Editor: David E.
A systematic screen for co-option of transposable elements across the fungal kingdom
Abstract How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1,237 genomes spanning the phylogenetic breadth of the fungal kingdom.
Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen
Abstract Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in one of the largest to date genome sequencing dataset spanning a worldwide collection of 1109 genomes from the major wheat pathogen Zymoseptoria tritici.
The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici
New Results doi: https://doi.org/10.1101/2023.07.16.549241 Abstract Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. LncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles.
Recurrent chromosome destabilization through repeat-mediated rearrangements in a fungal pathogen
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Recent reactivation of a pathogenicity-associated transposable element triggers major chromosomal rearrangements in a fungal wheat pathogen
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Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen
Niche characteristics of transposable element activation We focused on five TE families with particularly high copy numbers and evidence for large bursts to identify drivers of expansions (i.e., LINE/I RII_Cassini, LTRs RLG_Luna RLG_Sol, and RLC_Deimos, and the MITE DTX_MITE_Goblin). Even though RLG_Luna and RLG_Sol both contain among the highest copy numbers, they show no indication of recent bursts (Fig 6).
Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria
Editor's Pick Research Article | Ecological and Evolutionary Science Lea Stauber, Simone Prospero, Daniel Croll Aaron P. Mitchell, Editor DOI: 10.1128/mSphere.00737-20 ABSTRACT Emerging fungal pathogens are a threat to forest and agroecosystems, as well as animal and human health. How pathogens evolve from nonpathogenic ancestors is still poorly understood, making the prediction of future outbreaks challenging.
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
Abstract Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat.
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