Daniel Croll

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...

“groundbreaking” research indeed!

Thrilled to be hosting this session with @henriklicht.bsky.social and @agesiorska.bsky.social 🥳

Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩

Agreed, although I think baggage fees are more justified and can even be avoided with carry-on. Abstract fees must have a >99% profit margin. 🫠

SMBE2026 Symposium 3 | Genome plasticity and evolutionary innovation Organisers - Henrik H. de Fine Licht — University of Copenhagen, Denmark (Male) - Andi M. Wilson — University of Copenhagen, Denmark (Female) - Aleksandra Z. Gesiorska — University of Copenhagen, Denmark (Female) Invited Speaker - Daniel Croll — University of Neuchatel, Switzerland (Male)

Organisers
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen

Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel

Big congratulations @guidopuccetti.bsky.social !! Very proud of your achievement.

It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉

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...

Wonderful work! Congrats everyone!

Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.

tinyurl.com/5yx2wmz5

(1/n)

New record in Project funding SNSF Project funding reaches an all-time high with 1,451 applications and CHF 1.3 billion requested – while federal funding is stagnating.

The number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️

Evaluation is under way, and funding decisions will follow in spring 2026.

➡️ buff.ly/gEdD3OY

#research #science

Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® Pathogens’ responses to sudden temperature fluctuations, spanning various temporal scales, are critical determinants of their survival, growth, reproduction, and homeostasis. Here, we combined phenoty...

Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....