Guido Puccetti

k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence doi.org/10.1186/s128...

Heterochromatin epimutations impose mitochondrial dysfunction to confer antifungal resistance | The EMBO Journal imageimageHeterochromatin-island epimutations can provide resistance to caffeine and antifungal drugs in the fission yeast Schizosaccharomyces pombe. This study reveals that some epimutations cause re...

www.embopress.org/doi/full/10....

Our latest now online at EMBO Journal. Read if you are interested in how epimutations mediate antifungal resistance & how this might result in heteroresistance in human & cereal crop fungal pathogens. Big Thx & congrats to Andreas Fellas, Pin Tong & Alison Pidoux

And a big thanks to all coauthors!! @tbadet.bsky.social @DanielFlückiger, @Dominique Edel, @AliceFeurtey, @CamilleDelude, @mycomile.bsky.social @Stefano F. F. Torriani

A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen | mBio Sustainable food production requires the management of disease agents attacking crops. Application of antifungal compounds is among the key elements of pathogen containment; however, resistance can ri...

Finally out!
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...

A big thanks to @danielcroll.bsky.social & @GabrielScalliet

#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe

Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...

Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social
link.springer.com/article/10.1...

Cross-kingdom RNA trafficking from bacteria to fungi enables plant protection against fungal pathogens #research #MolecularPlant cell.com/molecular-pl...

Over many years, and a pandemic, we have worked with an international team of researchers to answer the question through genomics. We believe the origin is recent (in the last few decades, in line with previous research) and spatially from Western Europe

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus Author summary Cryptococcus is a genus of fungi that includes both pathogenic species capable of causing life-threatening infections in humans and many environmental species that inhabit soil, fruit, ...

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus journals.plos.org/plosgenetics...

Genomic traits associated with pathogenicity.

Lifestyles shape genome size and gene content in fungal pathogens.
buff.ly/tec1Tds

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....

Dissecting allele-specific fungicide resistance mechanisms by heterologous expression of the demethylase inhibitor target gene Cyp51 in a phytopathogen model BACKGROUND Fungicide resistance is a major concern both in agriculture and clinical disease control. Whilst several mechanisms of resistance have been elucidated, assigning phenotype to genotype is of...

WHY USE #YEAST AS A TOOL WHEN YOU'VE GOT STAGO?😁

Out now on @biorxivpreprint.bsky.social, our collab @theccdm.bsky.social led by @labkatz.bsky.social and Fran Lopez-Ruiz developed Parastagonospora nodorum as a tool to study #fungicideresistance genes.

www.biorxiv.org/content/10.1...

Widespread shifts in genome architecture and trophism across fungi. Phylogenetic positions of the shifts identified for genome size. Negative values denote an identified decrease in the genomic trait value while positive values denote an increase in the genomic trait value.

Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

I thought the Aspergillus fumigatus pan-genome was pretty wild when we started this project.

Aspergillus flavus said, "hold my beer..." Not only does it have a strong population structure with differences between environmental and clinical strains, only 58%of genes are conserved across the species!

Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host - Nature Microbiology A mycovirus infecting the pathogenic fungus Aspergillus fumigatus enhances its stress tolerance and virulence in mice.

🚨 Fungi + viruses + mammalian lungs? Buckle up! Our new paper in
@natmicrobiol.nature.com
uncovers the story of a deadly fungus and its gnarly viral hitchhiker — and how this duo may change how we diagnose & treat fungal disease 🍄🫁🚨 doi.org/10.1038/s415... ⬇️

Evolution of antifungal resistance in the environment - Nature Microbiology This Review discusses the evolution, emergence and expansion of environmental fungicide and antifungal drug resistance.

A little holiday news:

Evolution of antifungal resistance in the environment www.nature.com/articles/s41...

This started out as a little thought way back in early 2024 between @normanvanrhijn.bsky.social and I, and turned into a full on review! We hope it proves useful to the community.

A pangenomics-enabled platform for the high-throughput discovery of antifungal resistance factors in crop pathogens https://www.biorxiv.org/content/10.1101/2025.07.18.665620v1

Giant transposons promote strain heterogeneity in a major fungal pathogen | mBio No “one size fits all” option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for d...

We dive into the dynamics of #starships 🚀 in a fungal pathogen to ask: how might these giant #transposons impact human health? We find they drive genome-wide variation, encode clinically-relevant traits and even transpose within the same strain! 🍄🧪 out today in mBio #goteam doi.org/10.1128/mbio...

Super happy to see it out with all the hard work of everyone ! Such a nice story ! 🔥

It's been so many months that I have been postponing the publication of my poster's comics since I wanted to translate it (which I did not officially...), so why not doing it on the Labour Day ? 😅 It is now on Zenodo (French): doi.org/10.5281/zeno... 🧪🐡🎨

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Very excited with @tobybarilbio.bsky.social to share this preprint about his latest work on TEs!

We knew that TEs were very pretty active in this global fungal pathogen of wheat.

Now with nearly 2000 Illumina genomes available, we could finally ask questions about historic TE activation waves.

🔥 Exciting news! The first Symposium on Repeat-Induced Point mutations is happening June 30 – July 1 at the University of Neuchâtel🇨🇭!

🔹 Want to join? Register here > forms.gle/XWTd4gJAXZSx...

🚨 Limited spots available! So first come, first served!

🔹 More info > crolllab.github.io/ripm2025/

@guidopuccetti.bsky.social, Gabriel Scalliet and I are excited to share our latest work.

Resistance in agriculture emerges fast, but we fail to grasp how the myriad mutations in pathogen populations contribute to this.

Please check out and share our latest preprint: www.biorxiv.org/content/10.1...

From @guidopuccetti.bsky.social @danielcroll.bsky.social

Genomic Surveillance and Molecular Evolution of Fungicide Resistance in European Populations of Wheat Powdery Mildew Mutations conferring fungicide resistance to wheat powdery mildew emerged multiple times and are characterised by distinct geographic ranges in Europe and neighbouring regions.

Our paper on the evolution of fungicide resistance in wheat powdery mildew is now published! Congrats to all coauthors! doi.org/10.1111/mpp....

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Fungal phylogeny highlighting genome size changes

Summary of genome size variation among groups

@tbadet.bsky.social and I have a preprint out on transposon silencing in fungi!

Genome size evolution is fascinating and showcases the dynamic nature of transposon activation.

What we understand less are the dynamics of transposon defense systems encoded by the genomes.

doi.org/10.1101/2025...