Daniel Croll

The International Symposium on Cereal Leaf Blights isclb.com/registration in beautiful Banff from May 26-29 is approaching with a deadline for early registration/oral abstract due on March 31. @wheatinitiative.bsky.social

The latest work by @margaridasampaio.bsky.social is out as a preprint!

Using an eQTL dataset for the fungal wheat pathogen Zymoseptoria tritici, we asked whether new regulatory mutations had a predominant effect towards up- or downregulation.

Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen https://www.biorxiv.org/content/10.64898/2026.03.06.710201v1

Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen Abstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines.

Fouché, @oggenfussursula.bsky.social, McDonald & @danielcroll.bsky.social retrace chromosomal degeneration in a fungal pathogen, identifying the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles.

🔗 doi.org/10.1093/gbe/evag037

#genome #evolution

There is an old pattern that repeats itself when someone starts gaining visibility, sooner or later the narrative shifts.

This tends to be more noticeable for people who do not come from the traditional centers of power.

The only response is to keep working, keep building, and keep moving forward.

Please share widely! We think MycoMobilome can go a long way to support high-quality TE annotations across fungi!

Also, try it on your favorite 🍄 genome and tell us what you think 😉

#TEworldwide #TEsky

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

Need to annotate transposons in fungal genomes? 🧬
Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg...
Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social!

w/ @danielcroll.bsky.social

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism Abstract. Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal spec

Dauphin et al. assembled a telomere-to-telomere reference genome for an ectomycorrhizal fungus with a large, repeat-rich genome, showing its genome expansion was driven by a few lineage-specific TE families in recent history.

🔗 doi.org/10.1093/gbe/evag017

#genome #evolution #TEsky

Wishing everyone a propitious start into a prosperous, successful and happy year of the horse!

Thanks for making time for the visit @edelplopez.bsky.social ! I really enjoyed the time we got to chat science. We were very excited to hear your "crazy" ideas and can't wait to see the papers coming out!

Congrats!!

Hi everyone!
The talk I had the chance to give with @fnucleosome.bsky.social last October is now out on Youtube!
If you like evolution, 3D genomics, biodiversity and/or fungi, I think you might like it! 🧬🧪🍄
The submission of this paper has never been that close!

www.youtube.com/watch?v=Plez...

Headline: "Scientists discover emperor penguin colony in Antarctica using satellite images"

Yesterday it was cows using tools, today its penguins using satellite imagery.

1/🧵
Major milestone unlocked for mycology! 🍄

We just published a massive genomic resource in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐃𝐚𝐭𝐚, releasing 2,695 complete circular mitochondrial species assembled from public data

This single dataset nearly 𝐓𝐑𝐈𝐏𝐋𝐄𝐒 📈the known mitochondrial diversity of the Kingdom Fungi
rdcu.be/eYZ2h

Facultative heterochromatin mediated by core and accessory chromosome-encoded H3K27-specific methyltransferases controls virulence in a fungal phytopathogen Abstract. In many fungal phytopathogens, infection is regulated by accessory genomic regions enriched in facultative heterochromatin, but the precise role

Beyond excited to see this work finally out in @narjournal.bsky.social! We show that epigenetic modifiers on fungal accessory chromosomes can contribute to the overall epigenetic profile. Many thanks to @gomezlucia93.bsky.social and our other amazing collaborators 👏🏻

academic.oup.com/nar/article/...

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

Sharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...

PhD defense of David Marques, seen between his two PhD mentors, Ole Seehausen (left) and Laurent Excoffier (right). He is wearing a hat, which is traditional in Bern. It represents his PhD with an FST plot and sticklebacks.

David Marques at the wedding of his PhD sister, Joana Meier.

David carrying heavy gear on fieldwork with one of his study objects, a sea gull.

Earlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti...
Thanks to those who already shared the link!

Depends on the pathogen, I guess. However, generally, if the effector mutation that led to overcoming the R gene does not lead to a fitness or virulence penalty for the pathogen, that mutated allele wil be kept, and thus the R gene will not be "forgotten".

Welcome to Bluesky Leila @leilaebrahimi.bsky.social!

Genomic Insights into Historical Adaptation of Three Key Fungal Plant Pathogens Abstract. Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that c

Alkemade, @timbarra.bsky.social et al. did temporal association analysis on three major fungal crop pathogens collected between 1956 and 2023, identifying genes linked to fungicide resistance and stress responses as frequent sites of adaptation.

🔗 doi.org/10.1093/gbe/evaf241

#genome #evolution

Discovery of globally rare CYP51 mutations associated with azole resistance in Iranian Zymoseptoria tritici isolates - BMC Plant Biology Background Septoria tritici blotch, caused by Zymoseptoria tritici, is a major wheat disease worldwide. Demethylation inhibitor (DMI) fungicides, which target the sterol 14α-demethylase enzyme encoded...

link.springer.com/article/10.1...

Benjamin Adjei Croll lab at University of Neuchatel. PhD student

A very warm welcome to Benjamin Adjei!

pathogen-genomics.org/members/benj...

Hi! I am Mélanie, a new PhD student in the lab! Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...

A very warm welcome to Mélanie Echernier to the lab!

pathogen-genomics.org/2025/11/17/M...

Welcoming Joris to the Lab! Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...

A very warm welcome to the lab Joris Alkemade!

pathogen-genomics.org/2025/12/05/J...

Welcome to the lab, Jigisha! Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...

A very warm welcome to the lab Jigisha! @jigisha1.bsky.social

pathogen-genomics.org/2025/12/10/J...

Wonderful work Josje and Michael!! Big congrats on the publication!

Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social

www.cell.com/current-biol...