First day back after a great time in Belfast at #MicroSoc26 @microbiologysociety.org. Thank you to the organisers for the opportunity to present my work. Which, if you missed, is now currently available on bioRxiv!

fitness costs are associated with acquired antifungal resistance in N. glabratus, and these trade-offs can be targeted by drugs as shown by @gabaldonlab.bsky.social ➡️ link.springer.com/article/10.1...

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...

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

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution - Nature Ecology & Evolution Experimental evolution of fission yeast (Schizosaccharomyces pombe) in the same environment as a previous experiment with budding yeast (Saccharomyces cerevisiae) reveals parallel evolution but distin...

#NatMicroPicks

Same destination, different routes 🍄🧫🧪

Following 10,000 generations, parallel evolution occurred in separate yeast species, but took different genetic routes driven largely by transcriptomic and trans‑regulatory differences.

#MicroSky

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

www.biorxiv.org/content/10.1...
new preprint on predicting antifungal drug resistance in yeasts is out!

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 😉

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.

Cross-kingdom RNA interference promotes arbuscular mycorrhiza development - Nature Plants The authors provide evidence that symbiotic fungi forming widespread arbuscular mycorrhiza symbioses use cross-kingdom RNA interference to silence plant genes and promote their colonization of host ro...

Wow! Here's some solid evidence that arbuscular mycorrhizal fungi use small RNAs to regulate plant gene expression. Congratulations to the teams of @carogutj.bsky.social and Arne Weiberg

doi.org/10.1038/s414...

The human fungal pathogen Aspergillus fumigatus can produce the highest known number of meiotic crossovers Aspergillus fumigatus is a saprotrophic fungus that can cause serious life-threatening invasive infections in immunocompromised individuals. By constructing a recombination map, this study shows that ...

journals.plos.org/plosbiology/...

🍄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

Transcriptional and metabolic modeling analyses of developing Aspergillus fumigatus biofilms reveal metabolic shifts required for biofilm maturation | mSphere Aspergillus fumigatus is the most common etiological agent of a collection of diseases termed aspergillosis. Chronic and invasive manifestations of aspergillosis are highlighted by the development of biofilm-like structures on and in tissue. These biofilm structures are resistant to contemporary antifungal drugs, even for strains that are susceptible by standard antimicrobial susceptibility testing methods. Consequently, understanding the mechanisms by which A. fumigatus induces, develops, and maintains biofilms to evade antifungal therapies is expected to illuminate biofilm-specific therapeutic targets. Here, we identify genes involved in fungal fermentation and regulation of transcription as important mediators of A. fumigatus biofilm development.

“Transcriptional and metabolic modeling analyses of developing Aspergillus fumigatus biofilms reveal metabolic shifts required for biofilm maturation”

#microsky

Our new article is now online on @natplants.nature.com! ✨
We identified and characterised AvrPm4 and SvrPm4, a pair of powdery mildew effectors controlling avirulence on the wheat kinase fusion resistance protein Pm4 🌾 check it out ➡️ www.nature.com/articles/s41...

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...

Delighted to see the main work from my PhD finally published in @mbio.bsky.social! It all started with the observation that deleting the cutRS two-component system in S. venezuelae caused this amazing explorer phenotype in the presence of glucose. But what was going on?! (1/n)

Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth Nature Microbiology - During filamentous growth in the human fungal pathogen Candida albicans, a reduction in ribosome concentration leads to a decrease in macromolecular crowding. Inhibition of...

👉Excited to share our latest work @natmicrobiol.nature.com, revealing a decrease in cytoplasmic crowding during filamentous growth in the human fungal pathogen Candida albicans. Furthermore we found that inhibition of ribosome biogenesis can trigger filamentous growth in this pathogen
rdcu.be/eT1Su

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum Saccharomycotina yeasts are a highly diverse and widely distributed subphylum of ascomycete fungi that exhibit diversity in their asexual growth morphologies; the human commensal yeast Candida albican...

New preprint with @rokaslab.bsky.social! We used genomic, metabolic, environmental, and phenotypic data sets from 1,154 Saccharomycotina strains to asses filamentation variability and predict filamentation types across the subphylum. 🧩
www.biorxiv.org/content/10.1...

k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence doi.org/10.1186/s128...

Heterochromatin epimutations impose mitochondrial dysfunction to confer antifungal resistance | The EMBO Journal imageimageHeterochromatin-island epimutations can provide resistance to caffeine and antifungal drugs in the fission yeast Schizosaccharomyces pombe. This study reveals that some epimutations cause re...

www.embopress.org/doi/full/10....

Our latest now online at EMBO Journal. Read if you are interested in how epimutations mediate antifungal resistance & how this might result in heteroresistance in human & cereal crop fungal pathogens. Big Thx & congrats to Andreas Fellas, Pin Tong & Alison Pidoux

And a big thanks to all coauthors!! @tbadet.bsky.social @DanielFlückiger, @Dominique Edel, @AliceFeurtey, @CamilleDelude, @mycomile.bsky.social @Stefano F. F. Torriani

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...

Cross-kingdom RNA trafficking from bacteria to fungi enables plant protection against fungal pathogens #research #MolecularPlant cell.com/molecular-pl...

Over many years, and a pandemic, we have worked with an international team of researchers to answer the question through genomics. We believe the origin is recent (in the last few decades, in line with previous research) and spatially from Western Europe

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus Author summary Cryptococcus is a genus of fungi that includes both pathogenic species capable of causing life-threatening infections in humans and many environmental species that inhabit soil, fruit, ...

Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus journals.plos.org/plosgenetics...

Genomic traits associated with pathogenicity.

Lifestyles shape genome size and gene content in fungal pathogens.
buff.ly/tec1Tds

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....

Dissecting allele-specific fungicide resistance mechanisms by heterologous expression of the demethylase inhibitor target gene Cyp51 in a phytopathogen model BACKGROUND Fungicide resistance is a major concern both in agriculture and clinical disease control. Whilst several mechanisms of resistance have been elucidated, assigning phenotype to genotype is of...

WHY USE #YEAST AS A TOOL WHEN YOU'VE GOT STAGO?😁

Out now on @biorxivpreprint.bsky.social, our collab @theccdm.bsky.social led by @labkatz.bsky.social and Fran Lopez-Ruiz developed Parastagonospora nodorum as a tool to study #fungicideresistance genes.

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