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Thomas Badet

@tbadet.bsky.social
111 followers 84 following 6 posts

Junior researcher at the university of Neuchâtel - fungi enthousiast

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Reposted by Thomas Badet
bioRxivpreprint @biorxivpreprint.bsky.social · 11/08/2026
SAD-6/ATRX enables broad genome surveillance and defense in fungi www.biorxiv.org/content/10.64898/20…
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Thomas Badet @tbadet.bsky.social · 11/06/2026
Nearly a year after our symposium on Repeat-Induced Point (RIP) mutations, I’m happy to share the fruit of some of our discussions. The fungal RIP hypermutator mechanism has deep eukaryotic roots www.sciencedirect.com/science/arti... We hope to spark interest in this underappreciated mechanism.
Evolution of major eukaryotic genome defense systems.
The figure is organized along two axes representing core mechanistic features (homology recognition, small interfering RNA, and
heterochromatin assembly) and their lineage-specific elaborations. We hypothesize that a recombination-independent DNA
homology recognition system present in the eukaryotic common ancestor facilitated the emergence of both heterochromatin
assembly and small RNA-based repeat silencing. From this conserved ancestral core, lineage-specific gene neofunctionalizations
gave rise to distinct defense pathways: the RdDM pathway in plants; the piRNA and KRAB–ZFP pathways in vertebrates; and the
repeat-induced point mutation (RIP), methylation induced premeiotically (MIP), MSUD, and tandem repeat-induced sexual silencing
(TRISS) systems in filamentous ascomycete fungi. Question marks indicate steps for which the molecular mechanisms remain
unknown.
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Cecile Lorrain @ccilelorrain.bsky.social · 15/04/2026
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...
nature.com
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...
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Leon-Samuel Icking @lsi.bsky.social · 23/03/2026
🧬 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!
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Reposted by Thomas Badet
New Phytologist @newphyt.bsky.social · 06/01/2026
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/...
Bd21 and Bd21-3 display distinct lateral root emergence dynamics following root tip excision.
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Reposted by Thomas Badet
Guido Puccetti @guidopuccetti.bsky.social · 23/12/2025
link.springer.com/article/10.1...
link.springer.com
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...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 03/12/2025
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/10.64898/20…
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Guido Puccetti @guidopuccetti.bsky.social · 01/12/2025
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
journals.asm.org
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...
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Daniel Croll @danielcroll.bsky.social · 16/10/2025
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/...
journals.plos.org
Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom
Fungal genome size variation is largely driven by transposable elements and shaped by lineage-specific genome defense mechanisms. This study shows that the presence or absence of repeat-induced point ...
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PLOS Biology @plosbiology.org · 16/10/2025
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
 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.
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Pierre Grognet @pierregrognet.bsky.social · 07/07/2025
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
peercommunityjournal.org
Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina
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Josje Romeijn @jromeijn.bsky.social · 20/06/2025
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.
biorxiv.org
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Cecile Lorrain @ccilelorrain.bsky.social · 18/05/2025
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...
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Fabrizio Menardo @fmenardo.bsky.social · 05/05/2025
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...
doi.org
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...
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Thomas Badet @tbadet.bsky.social · 05/05/2025
🚨 Don't forget to register! 🚨 ℹ️ Deadline is set to May 23rd. 🔥 Many slots are still available.
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Thomas Badet @tbadet.bsky.social · 28/03/2025
🔥 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/
crolllab.github.io
RIPM 2025
Symposium on Repeat-induced Point Mutation research, 30.6 - 1.7, Neuchatel, Switzerland
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Daniel Croll @danielcroll.bsky.social · 25/03/2025
@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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Aaron Vogan @fungage-lab.bsky.social · 07/03/2025
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...
Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.
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Cecile Lorrain @ccilelorrain.bsky.social · 04/03/2025
Great talk @iglavincheska.bsky.social, exploring the impact of DNA methylation variation on the 3D genome structure of Zymoseptoria tritici! #ecfg17
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Francois Sabot @francoissabot.bsky.social · 03/03/2025
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...
biorxiv.org
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Aaron Vogan @fungage-lab.bsky.social · 11/02/2025
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...
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.
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Tatiana Giraud @tatianagiraud.bsky.social · 11/02/2025
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...
doi.org
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
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Jo Rhodes @drjorhodes.com · 17/01/2025
This looks a fascinating read!
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Pío Sierra @piosierra.bsky.social · 17/01/2025
TEs at work. Very interesting results.
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Daniel Croll @danielcroll.bsky.social · 16/01/2025
@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...
Fungal phylogeny highlighting genome size changesSummary of genome size variation among groups
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 14/01/2025
A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom www.biorxiv.org/content/10.1101/202…
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