Our raxtax tool for taxonomic classification is published: it is 2.7–100 times faster than competing tools but equally accurate - raxtax has increasing speedups with growing query and reference sequence numbers compared to existing tools: academic.oup.com/bioinformati...

DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form! 🧪🧬🦠🖥️ #secmet jointgeno.me/PortalStorie...

⏰ Closing soon! We're looking for a Research Scientist to work on novel platforms for sustainable myco-food production and precision fermentation. 💷 £37,500 to £40,240 🗓️ Apply by 30 November 2025 ➡️ buff.ly/WDsrbgl

Another fine outcome of my long-standing collaboration with Zhilin Yuan and Long Peng at RISF in Hangzhou: Endophytes with mycorrhizal potentials: biological and ecological implications - New Phytologist nph.onlinelibrary.wiley.com/doi/10.1111/...

🚨 PhD project offer linked to Fungarium Sequencing Project! Do you like bioinformatics? fungal genomics? historical DNA? check this out 👇 www.trees-dla.ac.uk/projects/imp...

I'm surprised I only came across it now, but this review on improving communication in data visualization is excellent. journals.sagepub.com/doi/10.1177/...

We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...

Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi www.biorxiv.org/content/10.1...

Fungal fossils tell a story of resilience: research by Worobiec et al. published in #FungalBiology (Aug 2025) traces dark septate endophytic (DSE) microsclerotia from the Eocene to today, revealing long-term plant–fungus associations. 👉 www.sciencedirect.com/science/arti...

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

New study from @mvanderheijden.bsky.social lab, showing that many commercial mycorrhizal inoculants are snake oil. So important for this data to be published! Between this, @lizkoziol.bsky.social and Matt Salomon’s work… well I think we make a strong point. onlinelibrary.wiley.com/doi/10.1002/...

🌿🍄‍🟫🌱🍄We’re recruiting!!🌿🍄‍🟫🌱🍄 I’m looking for two postdocs and a technician to join my group @sheffielduni.bsky.social @sheffieldpps.bsky.social to work with me on my exciting @royalsociety.org Faraday Discovery Fellowship project, details for each post as follows:

A quick tutorial blog on a method I haven't seen before to plot gene gain/loss from e.g. CAFE5 across a phylogeny - and clearly shows I always have fungi on the mind 🤓🍄 #rstats #ggplot2 rowena-h.github.io/data-visuali...

PHD: Based at the Earlham Institute with @neilhall.bsky.social and @rowenahill.bsky.social, and in collaboration with @rbgkew.bsky.social, we're seeking a #PhDstudent interested in #fungal #ecology and evolution to study functional diversity in root #symbiotic fungi. @aries-dtp.bsky.social

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes! www.biorxiv.org/content/10.1...

📣 Now announcing the journal publication 📄 of our work in @newphyt.bsky.social on how Verticillium undermines the plant's 🌱 "cry for help": terrific work by @antonkraege.bsky.social & @wolki95.bsky.social doi.org/10.1111/nph....

Our MARTi @nanoporetech.com paper is now out in @genomeresearch.bsky.social after several years of development (particularly Ned Peel and Sam Martin). We'd love to hear from users about how you're using it, or suggestions for new features. @earlhaminst.bsky.social genome.cshlp.org/content/earl...

PHD: What does an ‘optimal’ community of #bacteria and #fungi look like for #pathogen suppression? That's a key question to explore in this fully-funded #PhDproject with @neilhall.bsky.social, @mcmullan0.bsky.social and @rowenahill.bsky.social at the Earlham Institute.

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

PhD studentship Come help us understand the wheat rhizosphere at the Earlham Institute 🦠 Working at the interface of fungal antagonists & pathogens (@rowenahill.bsky.social @neilhall.bsky.social ), host genetic diversity (Simon Griffiths -JIC) and bacterial community diversity (Jacob Malone -JIC)

Want to understand how entire fungal chromosomes can be horizontally transferred? Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available. fungal-evolutionary-genetics.de/open-positio...

🍄 Today marks #UKFungusDay where we get to celebrate the weird and wonderful kingdom of Fungi. As well as being fundamental to a healthy ecosystem, and often fascinating to spot, #Fungi can be devastating to plant and animal populations.

Such a delight to share our work on the evolution of a cheese rind fungus in @currentbiology.bsky.social. This is the fantastic PhD work of @nicolasleonlouw.bsky.social and resulted from amazing collaborations, a wedding proposal(!), an undergrad course, & more! 🧵 www.cell.com/current-biol...

Was a pleasure to contribute a small part to this massive WGS effort of Kew's fungarium! @estergaya.bsky.social @rbgkew.bsky.social Check out the paper @newphyt.bsky.social 👉 doi.org/10.1111/nph.70472

THIS WEEK HAS SAUCE 4 Stunning fossils in sedimentary rocks reveal a new and co-oldest Early Cretaceous gilled mushroom-forming fungus Edaphagaricites conicus gen. nov. et sp. nov. academic.oup.com/botlinnean/a...

An opportunity of a lifetime for budding lichenologists. The National Trust and the Royal Botanics, Edinburgh are offering a PAID lichen traineeship in #Scotland! The work programme looks fascinating and a great opportunity to develop skills. Deadline: 3/10/2025. www.asva.co.uk/jobs/trainee...

It was a delight to have Guillaume Delhaye and Torda Varga (@rbgkew.bsky.social) at @earlhaminst.bsky.social last week, talking to a packed Norwich Research Park audience about mushroom-forming and mycorrhizal fungi from molecule to ecosystem! 🍄🧬🌳 @neilhall.bsky.social @norwichmicro.bsky.social

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

📣 NEW PREPRINT 📝 We identified evolutionary origins of many fungal effectors! We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression. www.biorxiv.org/content/10.1... cc @teamthomma.bsky.social

New #preprint from talented graduate student for a workflow we have been using for a while into a formal usage www.biorxiv.org/content/10.1...

Our paper mapping plant and mycorrhizal fungal diversity correlations is out! Relationships are weak at the global level, but both positive and negative at smaller scales. Plants are not always proxies for fungi — fungi need their own conservation focus @spun.earth @ethz.ch doi.org/10.1038/s414...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

💬 “We are taking genome #annotations from disparate methods and harnessing the information contained in them to produce a more unified set of annotations.” Comparing #genomes at scale with pan-annotation tools. buff.ly/TMOWcG8 @rowenahill.bsky.social 🧬 🖥️

Marine fungi culture collections (such as the one we have at @thembauk.bsky.social) are helping unlock the possibility for finding new solutions to many of the world’s biggest challenges 🌊🍄=💊🥓🪲 @uk.theconversation.com @plymbiomarsci.bsky.social @erc.europa.eu 👉 theconversation.com/marine-fungi...

🚨 Job Alert at RBG Kew! We are looking for Lab Research Assistants in genomics to join our Fungarium Sequencing Project! Do you like Fungi? Do you want to develop new -omics techniques? Interested in historical collections? Join the team! Posts to start ASAP. Apply here:https://lnkd.in/e2BpWJpA

Marine Fungi are found everywhere in the ocean. They are recyclers, a goldmine of compounds and symbiotic with other marine life. I chat about Marine Fungi in the BBC programme 'Secrets of the Sea'. Follow the link 👉 www.bbc.co.uk/programmes/p... @thembauk.bsky.social @plymbiomarsci.bsky.social

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

Our newest special issue is now live! Check it out to discover more about diverse and beautiful Fungi🍄🍄‍🟫🍄 On the cover: the fly agaric, Amanita muscaria, releasing its spores in the early morning light. www.cell.com/current-biol...

The #GENETICS June cover features an illustration of Starships, giant cargo-mobilising transposable elements found in fungal species of the subphylum Pezizomycotina. Starship elements are highly variable in overall length & genetic content. 1/2🧵

Our paper on phylogenetics of fungal Starship TEs is now on the cover of the June issue of Genetics @genetics-gsa.bsky.social 🙂 academic.oup.com/genetics/iss... @mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social

This #FungiFriday we want to share the latest issue of Field Mycology! This is the first issue to be edited by Kew Mycologist @clareblencowe.bsky.social and marks the publication now being #OpenAccess Check it out at fieldmycology.org

🍄The Last of Us - NIHR HPRU PhD opportunity🍄 Very exciting project on developing a genomic epidemiology toolkit for fungal outbreaks with @mcdonaldmeganc.bsky.social @drjorhodes.com @scalene.bsky.social and the Mycological Reference Lab Bristol www.findaphd.com/phds/project...

📢 JOB: Lead a landmark project to sequence 20,000 fungi & lichens from one of the world’s largest fungarium collections. Shape science, support biodiversity, and help safeguard our fungal future 🌍🧪 👉 careers.kew.org/vacancy/seni... 🗓️ Apply by 25 May #PlantSciJobs #fungi

This is wild. Chromosome distributions into different nuclei! Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi www.science.org/doi/10.1126/...

RAxML-NG v2.0 beta is here github.com/amkozlov/rax... Features 1. Difficulty prediction academic.oup.com/mbe/article/... 2. Adaptive search academic.oup.com/mbe/article/... 3. Early Stop www.biorxiv.org/content/10.1... 4. Model selection 5. Rapid bootstrapping academic.oup.com/mbe/article/...

Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?) doi.org/10.1093/g3jo... @mcmullan0.bsky.social @norwichmicro.bsky.social

The ancient psychedelics myth: ‘People tell tourists the stories they think are interesting for them’

📃 A new publication from @mcmullan0.bsky.social and the Hall Group studies pathogen genetic diversity to uncover how #crop #pathogens may be evolving in wild reservoirs. 🌱 buff.ly/I17w6p8 @neilhall.bsky.social

Fungal endophytes may not be a reliable way to improve plant resilience to global change. Warmer temperatures disrupt symbiosis between plants and fungal endophytes by reducing fungal colonization and diversity in plant tissues, with stronger effects in leaves than roots. dx.doi.org/10.1111/gcb....