Face of the guy who just pushed the "make myself even richer button" For context: www.youtube.com/watch?v=IHD8...

🔔 Our synthesis on what’s going on in the field of TE control and RIP in the fungal world! Out now in Trends in Genetics!

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.

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

Exactly this.

Spent this week with an amazing cohort of Scandavian and Baltic PhD students. NOVA is a wonderful tradition and the future for plant 🌱 pathology 🍄 is bright! ☺️

So proud to see this story finally out!🎉 We added new data since our previous preprint—transgenic barley plants with an engineered immune receptor that fights off two fungal pathogens at once. Short 🧵 and link to the original preprint thread on X👇 www.science.org/doi/10.1126/...

We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky

Talks (Part 1): @danielcroll.bsky.social @jrotwitguez.bsky.social Aaryan Bhatia @mtoll8.bsky.social Ana Lindeza Máire Ní Leathlobhair @iglavincheska.bsky.social @marcelauliano.bsky.social Julien Dutheil @a-mack-s.bsky.social Shu Zhang

Thrilled to see this finally out!! Our new work suggests #Starships helped #Colletotrichum acquire the genes needed to infect lupin. A glimpse into how fungal pathogens emerge through horizontal transfer and genome reshaping. biorxiv.org/content/10.6... #Fungi #Genomics #Pathogenicity #evolution

Out Now! Pooled CRISPRi screening reveals fungal-specific drug target candidates #MicroSky

Wonderful thread and thinking on (bacterial) pangenomes

New preprint out! We generated haplotype-phased genome assemblies for two poplar rust fungi. These resources open new opportunities to explore rust genome architecture, haplotype diversity, and TE-driven evolution. www.biorxiv.org/content/10.6...

I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland. Please interpret with caution. By segment: S: nextstrain.org/groups/hodcr... M: nextstrain.org/groups/hodcr... L: nextstrain.org/groups/hodcr...

Genomepanel_nf v 1.0.8 is out! Includes a nice summary html in addition to the tsv files, more robust GATK implementation, even more aggressively saves on storage space and includes now a fully functional example dataset. crolllab.github.io/genomepanel_... Please get in touch if you have feedback.

📢 EffectorGeneP is finally here! Stop missing small, single-exon or orphan genes from your favourite pathogen genome. Current tools only annotate 15%-78% of effector genes, EffectorGeneP finds 95% - including the large AvrSr26 family in stem rust. #Bioinformatics 📖 www.biorxiv.org/content/10.6...

There's a story behind every project that doesn't get fully captured in the final paper. Check out our "behind the paper" accompanying our paper on convergent evolution of aerobic fermentation in yeast. communities.springernature.com/posts/learni... @hittingerlab.bsky.social @rokaslab.bsky.social

Delighted to see this work out in #ScienceAdvancesResearch @science.org where we uncover a surprising evolutionary origin of fungal effector proteins as ancient antimicrobials. Led by the super-star @mesny.bsky.social in the frame of @ceplas.bsky.social @mibinet.bsky.social & @madfungi.bsky.social

🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @science.org @teamthomma.bsky.social www.science.org/doi/10.1126/...

Professor in Epidemiology/Pathology for Agricultural Crop Plants at Aarhus University www.au.dk/om/stillinge...

Excited to have Carlos Lax @clax8.bsky.social and Ghizlane Tahiri @ghizlane-tahirizn.bsky.social recently join our lab. Give them a follow to not miss out on their fantastic science!

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Amazing new tool out by @tobybarilbio.bsky.social ! We think this is going to be a super useful tool to annotate TEs in a pangenome context!

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵 #TEworldwide #transposableelements #bioinformatics #genomics

Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache! Here's my solution that used to be lab-internal but that I am happy to share: crolllab.github.io/genomepanel_...

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1/11 🔥 New preprint alert 🔥 We wanted to know what plants in the wild really care about. So we asked them 🎤. Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations” www.biorxiv.org/content/10.6...

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

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

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

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!

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...

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

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...

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!

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!

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