iiinova — where your digital self keeps evolving

We have a postdoc position on "Evolution of cross-kingdom RNA crosstalk". The project is on sRNA evolution in plant pathogens studied via pangenomics. You find the full ad here: pathogen-genomics.org/jobs/ Happy to answer any question! Please spread the word to anyone who might be interested.

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We have a postdoc position on "Fungal population genomics" focused on domestication and co-invasion processes in diverse fungi. You find the full ad here: pathogen-genomics.org/jobs/ Happy to answer any question! Please spread the word to anyone who might be interested.

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We have a postdoc position on "Beetle-fungus co-invasion genomics" looking at ambrosia beetle/fungi symbionts across the globe. Collab with WSL Zurich. You find the full ad here: pathogen-genomics.org/jobs/ Happy to answer any question! Please spread the word to anyone who might be interested.

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We have a postdoc position on "Deep learning for evolutionary genomics" with a focus on genome structure evolution, introgression detection and more. You find the full ad here: pathogen-genomics.org/jobs/ Happy to answer any question! Please spread the word to anyone who might be interested.

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Daniel Croll @danielcroll.bsky.social · 11/04/2025

Excited to do a postdoc in beautiful Neuchatel / Switzerland🇨🇭? We have several postdoc positions open at the moment! Check our website for the full ads here: pathogen-genomics.org/jobs Happy to answer any question and please spread the word to anyone who might be interested!

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I will join this great Summer School on Plant Pathogenomics for a Sustainable Future of Food. End of June in beautiful Bologna! 🇮🇹 Share with your interested colleagues and don't miss the application deadline 😉 www.2p4s2f.com

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We tried to tie together the timing of a TE family expansion with potential adaptive functions. These could be linked to fungicide resistance gains or other pathogen traits.

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A large and diverse number of TE families show high variation in copy number among populations. The variation in TE numbers often tracks the expansion out of the pathogen's origin in the Middle East. We then focused on the TEs showing the most dramatic recent expansions across the genome.

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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.

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Daniel Croll @danielcroll.bsky.social · 04/04/2025

Marie Curie Postdoctoral Fellowships (MSCA) Excited by fungi, genomes, transposons, sustainable agriculture, microbiomes or other topics? Looking for a friendly and interactive lab located in one of the most beautiful towns in Switzerland? 🇨🇭⛰️⛵ Get in touch and please share! pathogen-genomics.org

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We just had an amazing group of BSc block course students hosted in our lab. University of Neuchatel #UNINE has the best students! 😊💪🧑‍🎓

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Daniel Croll @danielcroll.bsky.social · 02/04/2025

So happy - our lab just had two PhD students graduating within the span of a week! Biggest congrats to @guidopuccetti.bsky.social and Sarai Reyes-Avila!! 🎉🧑‍🎓🧑‍🎓🎉 Best wishes from all of us for your future paths!

Guido Puccetti explaining his PhD research on fungicide resistance

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Daniel Croll @danielcroll.bsky.social · 02/04/2025

Summer time is here and I get to see the last sunrays again on my cycle home! 🚲🗻

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Finally, we assessed the impact on resistance by one of the newly discovered and highly resistant Irish Cyp51 haplotypes using mutant constructs.

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The molecular target encoded by the Cyp51 locus presented a very complex landscape of overlapping associations depending on the exact DMI. Structural variation is seemingly also playing a role.

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Our key outcome is a large atlas detailing demethylation inhibitor (DMI) resistance loci in the large European diversity panel. We confirmed the dominant role of modifications in the molecular target Cyp51, but also mapped a vast number of additional loci making contributions to DMI resistance.

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GWAS can be very powerful in diverse populations such as found for Zymoseptoria tritici. So, we made sure to comprehensively capture genetic variation combining SNP, Kmer and structural variant based genotyping.

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In painstaking work, we arrayed all these strains for genome sequencing and assessment of resistance levels. We used both colony growth reductions and half maximum concentrations (EC50) as complementary metrics for resistance.

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Our key step was to build a 1400-strain panel of Zymoseptoria tritici strains collected over 15 years and across over 27 countries. This is thanks to a large resistance monitoring effort across Europe.

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Daniel Croll @danielcroll.bsky.social · 14/03/2025

@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...

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What better way to spend the day than having one of my favorite scientists visit us in Neuchâtel 🇨🇭 Thanks so much @cedricfeschotte.bsky.social for taking time and giving a stellar seminar! Lots of inspiring chats about our mutual passion for transposons. Keep enjoying your time in Switzerland!

Cedric Feschotte, Ursula Oggenfuss and Tobias Baril at the Neuchâtel castle

Cedric Feschotte and Daniel in front of the cathedral

Cedric's seminar on paradigm shifts in transposon research

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Daniel Croll @danielcroll.bsky.social · 24/01/2025

Neuchâtel 🇨🇭just before sunrise

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Finally, we hypothesized that additional mutation signatures should be out there in fungal genomes hinting at RIP-related defense systems. We found indeed some very interesting mutation enrichment patterns suggesting that we do not know the full extent of such defense system.

Screen for mutation signatures across fungi

Enrichment in RIP-like signatures in ascomycetes

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RIP targets any duplicated sequence and creates point mutations in both copies at astonishing rates. Any recent copy of a transposon should become deactivated. The RIP machinery is not yet very well understood though. So, we used the phylogenetic framework to predict possibly missed RIP components.

RIP components and association with genome features

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RIP loss also coincided with a genome expansion in the group of plant pathogens including Blumeria graminis f.sp. tritici.

Genome size shifts in the Blumeria genus

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We based our work on a thousand fungal species dataset to identify shifts in genome sizes. We identified some remarkably fast shifts, which happened after the loss of a transposon defense system called RIP. RIP is a not yet well understood transposon defense system first described in Neurospora.

Correlates of genome size shifts across the phylogeny

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