Genome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature Plants This study introduces genome–host association (GHA), leveraging natural epidemics to map the genetic landscape of host adaptation in the pathogen Zymoseptoria tritici. Applied to 832 wheat fungal stra...

Thrilled to share our paper now out in Nature Plants 🎉
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.

www.nature.com/articles/s41...

🧬 Please repost 🧬

I was asked to organise a panel discussion for a SynBio Student Meetup in Hamburg in the middle of May and I'm still looking for panellist! If you know any researchers at the PhD/Postdoc who have expertise in metabolic/genome/multicellular organism engineering, please reach out!

Bd21 and Bd21-3 display distinct lateral root emergence dynamics following root tip excision.

Root tip excision-induced exodermis lignification impacts lateral root emergence in Brachypodium distachyon

Bellande et al. @joopvermeer.bsky.social @tbadet.bsky.social @anneroulin.bsky.social @rootcap.bsky.social

nph.onlinelibrary.wiley.com/doi/10.1111/...

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...

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system www.biorxiv.org/content/10.64898/2025.12...

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

Very excited to see the final version of our kingdom-scale fungal genome defense manuscript out in @plosbiology.org !

This work has been a major project of @tbadet.bsky.social during his time in our lab.

We hope to stimulate much more exciting work on fungal TEs.

journals.plos.org/plosbiology/...

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

Our description of the transcriptomic changes during sexual development in #Podospora anserina is out in @genomics.peercommunityin.org ! peercommunityjournal.org/articles/10....
@i2bcparissaclay.bsky.social @univparissaclay.bsky.social

The first paper of my PhD is now available as a preprint! 🎉

Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.

Excited to share the first PhD preprint of @iglavincheska.bsky.social — now on bioRxiv!
We explored the 3D genome of Zymo and found:
🧬 Rabl-like conformation
🧩 Accessory chr tethered to core centromeres
🏰 Self-interacting domains and boundaries with insulator motifs
www.biorxiv.org/content/10.1...

Population genomics and molecular epidemiology of wheat powdery mildew in Europe Agricultural diseases are a major threat to sustainable food production. This study of wheat powdery mildew, a disease caused by the fungus Blumeria graminis, shows that the population structure can b...

Very happy to see our paper online: "Population genomics and molecular epidemiology of wheat powdery mildew in Europe". Congrats to @jigisha1.bsky.social and all coauthors! doi.org/10.1371/jour...

🚨 Don't forget to register! 🚨

ℹ️ Deadline is set to May 23rd.

🔥 Many slots are still available.

And shoutout to the other members of the organising committee @oggenfussursula.bsky.social and @danielcroll.bsky.social

🔥 The event will bring together molecular biologists, evolutionary geneticists, and bioinformaticians to explore RIP’s role in transposable element control, genome integrity, and fungal adaptation.

Looking forward to seeing you in Neuchâtel! 🏔️ #RIPM2025 #FungalGenomics #EvolutionaryBiology

🔥 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...

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...

Great talk @iglavincheska.bsky.social, exploring the impact of DNA methylation variation on the 3D genome structure of Zymoseptoria tritici!
#ecfg17

Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪

In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5

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

Illustration of FuSpok killing a cell which has lost an accessory chromosome. Core chromosome in blue, accessory chromosome in red. Black circle: FuSpok. Green circle: antidote function. Red triangle: toxin function.

Interested in #fungal accessory chromosomes or toxin/antidote genes? Check out our new preprint! We show that the Spok gene family in Fusarium include active toxin/antidote genes. We present a model for how these genes influence the evolution of fungal genomes. www.biorxiv.org/content/10.1...

An inversion polymorphism under balancing selection, involving giant mobile elements, in an invasive fungal pathogen Abstract. Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by

An inversion polymorphism under balancing selection, involving giant mobile elements, in the invasive fungal pathogen responsable for the chesnut blight disease!
doi.org/10.1093/molb...

This looks a fascinating read!

TEs at work.
Very interesting results.

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...

A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom www.biorxiv.org/content/10.1101/2025.01....