Reposted by Thomas BadetbioRxivpreprint @biorxivpreprint.bsky.social · 11/08/2026SAD-6/ATRX enables broad genome surveillance and defense in fungi www.biorxiv.org/content/10.64898/20… 011
Thomas Badet @tbadet.bsky.social · 11/06/2026Nearly 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. 14622
Reposted by Thomas BadetCecile Lorrain @ccilelorrain.bsky.social · 15/04/2026Thrilled 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.comGenome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature PlantsThis 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... 35231
Reposted by Thomas BadetLeon-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! 028
Reposted by Thomas BadetNew Phytologist @newphyt.bsky.social · 06/01/2026Root 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/... 054
Reposted by Thomas BadetGuido Puccetti @guidopuccetti.bsky.social · 23/12/2025link.springer.com/article/10.1...link.springer.comDiscovery of globally rare CYP51 mutations associated with azole resistance in Iranian Zymoseptoria tritici isolates - BMC Plant BiologyBackground 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... 074
Reposted by Thomas BadetbioRxiv Genomics @biorxiv-genomic.bsky.social · 03/12/2025A 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… 068
Reposted by Thomas BadetGuido Puccetti @guidopuccetti.bsky.social · 01/12/2025Finally 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 #Europejournals.asm.orgA large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen | mBioSustainable 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... 12611
Reposted by Thomas BadetDaniel Croll @danielcroll.bsky.social · 16/10/2025Very 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.orgPhylogenomic signatures of repeat-induced point mutations across the fungal kingdomFungal 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 ... 04215
Reposted by Thomas BadetPLOS Biology @plosbiology.org · 16/10/2025Fungal #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 03526
Reposted by Thomas BadetPierre Grognet @pierregrognet.bsky.social · 07/07/2025Our 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.socialpeercommunityjournal.org Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina 046
Reposted by Thomas BadetJosje Romeijn @jromeijn.bsky.social · 20/06/2025The 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 710245
Reposted by Thomas BadetCecile Lorrain @ccilelorrain.bsky.social · 18/05/2025Excited 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... 01711
Reposted by Thomas BadetFabrizio Menardo @fmenardo.bsky.social · 05/05/2025Very 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.orgPopulation genomics and molecular epidemiology of wheat powdery mildew in EuropeAgricultural 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... 1159
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. 021
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.ioRIPM 2025Symposium on Repeat-induced Point Mutation research, 30.6 - 1.7, Neuchatel, Switzerland 288
Reposted by Thomas BadetDaniel 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... 22815
Reposted by Thomas BadetAaron Vogan @fungage-lab.bsky.social · 07/03/2025We 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... 3256136
Reposted by Thomas BadetCecile Lorrain @ccilelorrain.bsky.social · 04/03/2025Great talk @iglavincheska.bsky.social, exploring the impact of DNA methylation variation on the 3D genome structure of Zymoseptoria tritici! #ecfg17 0123
Reposted by Thomas BadetFrancois Sabot @francoissabot.bsky.social · 03/03/2025Do 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 1107
Reposted by Thomas BadetAaron Vogan @fungage-lab.bsky.social · 11/02/2025Interested 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... 1289
Reposted by Thomas BadetTatiana Giraud @tatianagiraud.bsky.social · 11/02/2025An 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.orgAn inversion polymorphism under balancing selection, involving giant mobile elements, in an invasive fungal pathogenAbstract. Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by 185
Reposted by Thomas BadetPío Sierra @piosierra.bsky.social · 17/01/2025TEs at work. Very interesting results. 031
Reposted by Thomas BadetDaniel 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... 47946
Reposted by Thomas BadetbioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 14/01/2025A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom www.biorxiv.org/content/10.1101/202… 0106