How do fungi distinguish conspecific self from non-self? The genetics of this fascinating topic are plagued with misunderstandings even amongst mycologists. We wrote a review/rant to address this confusion, out now! 🍄 #fungi #allorecognition #HETgenes www.sciencedirect.com/science/arti...

Drawing the line: Clarifying fungal allorecognition from HET domains to het genes to heterokaryon incompatibility

The iconic networks of filamentous fungi are connected through hyphal fusions. While fusion is beneficial among hyphae from the same fungal individual…

sciencedirect.com

I’ve seen trees you people wouldn’t believe. Deep branches collapsing off the shoulder of a saturated site, unresolved. I watched long-branch attraction glitter in the dark near the root of the Archaea. All those topologies will be lost in time… like tips in a polytomy.

NOD-like receptor genes undergo diversity-enhancing evolution in a fungal species complex academic.oup.com/gbe/advance-...

NOD-like receptor genes undergo diversity-enhancing evolution in a fungal species complex

Abstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria

academic.oup.com

Ugh #pangenome #bioinformatics #genomics

Applications to the Gordon Research Seminar in Speciation are now open! We encourage PhD students & postdocs from all geographies, backgrounds, disciplines to APPLY! This 2d seminar in beautiful Lucca 🇮🇹 will be followed by a 5d conference open to the broader community. www.grc.org/speciation-g...

#Mosquito gene drives for #malaria control can be undermined by rare, hard to detect genetic resistance alleles. This study by @ioannamor.bsky.social @drew-hammond.bsky.social &co reveals how #CRISPR resistance emerges and how to overcome it, advancing vector control 🧪 #AcademicSky plos.io/3R0ggEQ

Me trying to run minigraph-cactus to be like the cool pangenome kids #Pangenome #genomics

I talked about this at PEQG a few weeks ago. In addition to github.com/RILAB/argprep (preps your genome assemblies for SINGER), argtest github.com/RILAB/argtest does some QC to clean up an ARG estimated with SINGER.

Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea https://www.biorxiv.org/content/10.64898/2026.06.24.733965v1

ERGA member Merce Montoliu Nerin @mmontonerin.bsky.social will present @official-smbe.bsky.social June 29 in session "L04 – Understanding adaptive evolution through the lens of hologenomics" #SMBE2026

kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions https://www.biorxiv.org/content/10.64898/2026.06.21.732238v1

"Enabling the prediction of phage receptor specificity from genome data" #genomics #immunity #bacteria #viruses www.biorxiv.org/content/10.6...

Enabling the prediction of phage receptor specificity from genome data

Predicting which receptor a phage binds to from genome sequence alone has remained an intractable challenge, principally because the experimental phenotypic data required to train and validate predict...

biorxiv.org

1/8 What if the genomic features we associate with fungal pathogens were also used by mutualists? We assembled 41 scale lichen genomes across 11 Peltigera species with 30 chromosome scale and 5 T2T revealing an unexpected genomic toolkit behind lichen symbiosis. doi.org/10.64898/202... #lichen

A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi

Fungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition,...

doi.org

🗞️New Paper🗞️ We show that #Candida & #Staph cooperate via copper handling - with fungal copper uptake & bacterial copper export shaping the community. @mrccmm.bsky.social @microbiologysociety.org @universityofexeter.bsky.social www.microbiologyresearch.org/content/jour...

Copper-driven mutualism of Candida albicans and Staphylococcus aureus interkingdom biofilms

Although fungi and bacteria commonly co-exist within polymicrobial communities, the molecular mechanisms underlying their interactions are still not well understood. Here, we show that the fungus Cand...

microbiologyresearch.org

"Unifying Repbase and Dfam: a new open foundation for transposable element research" #genomics #transposons link.springer.com/article/10.1...

Unifying Repbase and Dfam: a new open foundation for transposable element research - Mobile DNA

Repbase and Dfam, the two foundational resources for transposable element annotation, are being unified into a single, fully open access framework, with Repbase released under CC-0 and its core curati...

link.springer.com

This very interesting paper shows the degree to which speciation research is now dominated by genomic approaches, and argues (among other things) that since it's an unreliable way to measure reproductive isolation (RI), we should place less emphasis on it. academic.oup.com/evolinnean/a...

The identity crisis of speciation genomics

Abstract. Understanding how reproductive isolation (RI) evolves remains a central goal of speciation research. Quantifying RI is challenging, and researche

academic.oup.com

Reproductive isolation emerges from coordinated barriers during mating system divergence in plants https://www.biorxiv.org/content/10.64898/2026.04.26.720968v1

Where do plant pathogen effectors come from? @mesny.bsky.social shows how fungi turned shield 🛡️ into sword ⚔️ to end up with dual-function molecules to disrupt host immunity & protective host microbiota. @ceplas.bsky.social @mibinet.bsky.social @madfungi.bsky.social www.science.org/doi/10.1126/...

Plant-associated fungi co-opt ancient antimicrobials for host manipulation

Fungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.

science.org

Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change @naturecomms.bsky.social www.nature.com/articles/s41...

Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change - Nature Communications

Genetic load is often overlooked in conservation predictions of species response to climate change. This study found that effective population size was the major determinant of genetic load and that g...

nature.com

I'm finding this little pipeline to get trees out of BUSCO runs quite convenient #phylogenomics github.com/jamiemcg/BUS...

GitHub - jamiemcg/BUSCO_phylogenomics: BUSCO_Phylogenomics | Pipeline to construct species phylogenies using BUSCO proteins

BUSCO_Phylogenomics | Pipeline to construct species phylogenies using BUSCO proteins - jamiemcg/BUSCO_phylogenomics

github.com

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

rambaut/figtree

Automatically exported from code.google.com/p/figtree - rambaut/figtree

github.com

"TAIR 12 is here!" Read more here: https://arabidopsis.org/news/breaking-news#307 #News

Plasmids use immune systems like #CRISPR-Cas to compete with other #plasmids, but do these systems confer an advantage? @davvi36.bsky.social &co show that CRISPR-Cas benefits resident plasmids but is constrained by toxin-antitoxin systems after horizontal transfer @plosbiology.org 🧪 plos.io/4qNbdDt

🐟💃

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 6mo ago

Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish https://www.biorxiv.org/content/10.64898/2026.02.16.706123v1

So I did something a bit different :). Thrilled to see this fun project out! 🐟 #genomics "Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish" www.biorxiv.org/content/10.6...

I submitted this ms to a journal about a 1.5 months ago, and the status remains "Awaiting Referee Assignment". The editor says they are struggling to find a second reviewer... Are these waiting times normal? Should I offer a fresh list of potential reviewers or is that inappropriate? 💔 #postdoclife

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 10mo ago

NOD-like receptor genes evolve under diversity-enhancing mechanisms in a fungal species complex https://www.biorxiv.org/content/10.1101/2025.09.29.679196v1

Are you excited about pangenomics? If so, join us in Edinburgh on 8-9th June to discuss the latest methods & insights from using these approaches across biodiversity! More details here: royalsociety.org/science-even... Organised together with @henrylnorth.bsky.social & @joanameier.bsky.social!

Pangenomics transforms evolutionary biology | Royal Society

This Theo Murphy meeting organised by Dr Joana Meier, Dr Henry North and Dr Charlotte Wright, will showcase cutting-edge pangenome tools, applied uses of pangenomes which are transforming health and a...

royalsociety.org

Would you say that Neurospora crassa is declining as a model organism for fungal biology? 💛 No way, that orange fun-guy is alive and well! 🔴 Yeah, not so many people work with it nowadays ... 🔵 Neuro-who? 📅 Ends: December 31, 2025, 10:03 PM UTC 📊 Show results

Whoop! New preprint has dropped - led by the amazing @trevormugoya.bsky.social. We developed a SV-calling and benchmarking platform called SaVor and test it on 1,165 Arabidopsis thaliana short read whole genomes. Do check out the paper, and try SaVor on your own data: github.com/ChabbyTMD/Sa...

GitHub - ChabbyTMD/SaVor: A flexible snakemake structural variant calling workflow.

A flexible snakemake structural variant calling workflow. - ChabbyTMD/SaVor

github.com

bioRxivpreprint@biorxivpreprint.bsky.social · 8mo ago

SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data https://www.biorxiv.org/content/10.1101/2025.11.26.690832v1

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system https://www.biorxiv.org/content/10.64898/2025.12.02.690432v1