📣...and now for something completely different: no plant pathogens, no Verticillium, but lichens! Driven by our lichen king🤴@ciarankelly.bsky.social with help of a.o. @hroevenich.bsky.social @usadellab.bsky.social @vivienrosenthal.bsky.social Watch for more in future! www.biorxiv.org/content/10.6...

Decoupled evolution of antimicrobial repertoires in lichen-forming fungi

Lichens are stable multipartite symbioses in which a fungal mycobiont associates with one or more photosynthetic partners while hosting complex microbiomes. Secreted antimicrobial proteins (AMPs) have...

biorxiv.org

Ciaran Kelly@ciarankelly.bsky.social · 3w ago

Our new preprint is out! 🍄 Decoupled evolution of antimicrobial repertoires in lichen-forming fungi We compared many lichen-forming fungal genomes to ask how different photobiont associations relate to their antimicrobial repertoires.

It’s a wrap! What an inspiring #IAL10 full of amazing talks, lively discussions, and wonderful people to meet. Heading back to Germany with lots of fresh ideas to explore in my favourite Peltigera lichens. Proud to have represented @mibinet.bsky.social at IAL together with @ciarankelly.bsky.social

A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi https://www.biorxiv.org/content/10.64898/2026.06.16.732702v1

This was the magnum opus of @vivienrosenthal.bsky.social within @mibinet.bsky.social with the labs of @faltegoer.bsky.social @teamthomma.bsky.social Yukioyo Sato François Lutzoni Silke Werth and Markus Pauly

8/8 Thus, pathogenic and mutualistic fungi might share a genomic grammar-compartmentalized genomes, mobile-element-driven diversification, and expanded recognition & signaling repertoires. Is this just an ancestral genomic toolkit - with ecology deciding the outcome or is there yet more to discover?

7/8 Does the genomic toolkit actually get used? Layer-specific RNA-seq of a P. rufescens thallus seems to indicate so: Pth11 GPCRs, peptidase antimicrobial proteins and a LEC-1-like galectin all light up in the cortex/photobiont layer - the symbiotic interface.

6/8 Structure-based search finds ~103 GPCRs per genome - vs 26 with old sequence methods in Cladonia. 76% are Pth11-like (CFEM) receptors. These are often found in plant pathogens as well …the plot thickens further.

5/8 But there is more lichens as an untapped antimicrobial reservoir? ~306 antimicrobial candidate proteins per genome on average. Profiles are species-specific and remarkably stable, with lineage-specific expansions and the tripartite species carry the biggest catalogues.

4/8 And lurking in those plastic, repeat-rich regions: Starship-like elements - sometimes close to virulence-associated orthologs. Big mobile elements doing their big mobile-element things.

3/8 But there seems to be a pathogen parallel we didn't really expect in a mutualist: secreted-protein genes sit significantly closer to transposable elements than other genes in the genomes. That looks like the "two-speed genome" of plant pathogens… in a lichen.

2/8 Genome size ranges from a small 56 Mb (P. didactyla) to 145 Mb (P. aphthosa) - and almost all of that difference is transposable elements.

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

What an incredible few weeks it’s been! I had many great discussions during my poster presentation at #Fungal26 in beautiful Pacific Grove. Right after, I attended @vaam-microbes.bsky.social 2026 in Berlin, where I had the honor of giving a talk on my absolute favorite topic (lichens, of course!)

Happy to share our recent preprint: "DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity" www.biorxiv.org/content/10.6... @spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social

Thrilled to share our work on Alkekengi officinarum at SolRub 2025 in beautiful Turin!

60+ flow cells in action! Our PromethlON has been cranking out huge data lately🧬 #nanopore #DNAsequencing @nanoporetech.com @usadellab.bsky.social

If my tattoo doesn't scream “Team Plant” 🌱, then I don't know. Enjoyed our time at the @pacbio.bsky.social party ! #PAG32 #PAG #TeamPlant @usadellab.bsky.social @lucasmunnes.bsky.social

For all the plant people at #pag32. We are currently losing at the @pacbio.bsky.social booth. Come and save our pride! 💪🏼🌱

My first PAG conference in San Diego. Thank you for giving me the opportunity to talk about Alkekengi officinarum (Chinese lantern plant) and its ornamental value! @rfinkers.bsky.social #PAG #PAG32 @usadellab.bsky.social @angelakranz.bsky.social @lucasmunnes.bsky.social

The first day was a lot of fun presenting our new Use Case LichenMetaImage, a collaborative approach of @nfdi4bioimage.bsky.social @nfdi4plants.bsky.social and @nfdi4microbiota.bsky.social , at the NFDI4Microbiota conference in Leipzig !

Very happy to share the latest publication from @usadellab.bsky.social presenting the first high-quality chromosome-scale genome assembly of blackcurrant. This enabled the study of transcriptomic responses of blackcurrant to drought stress. academic.oup.com/hr/advance-a...

A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Ribes nigrum L.)

Abstract. Blackcurrant (Ribes nigrum L., family Grossulariaceae) is a perennial shrub that is widely cultivated for its edible berries. These are rich in a

academic.oup.com

No growth chamber? No problem! Just throw out the lab coats, claim the cabinet, install some lighting and put in your plates. Voilà you have your DIY growth chamber. Works better than expected 😅

What a pleasure to be at DGHM & VAAM 2024 . I am looking forward to nice presentations and scientific discussions!

with @vivienrosenthal.bsky.social lichen project!

NFDI4Microbiota@nfdi4microbiota.bsky.social · 3y ago

🔬 Exciting Update on #NFDI4Microbiota Use Cases! Explore 3 new Use Cases #MicroBioKG, #LichenMetaImage, and #VirJenDB and join our Use Case presentations on March 26th, 1-2:30 PM CET Zoom-Meeting: 630 7779 8681, Passcode: 973383.

Another fantastic talk at the #PlantACT conference at @hhu.bsky.social . Katherine Denby from the University of York on "Elucidating and re-wiring gene regulatory networks to enhance crop disease resistance".

Nice talk by Edoardo Puglisi at the PlantACT conference at HHU. His research is on beneficial rhizosphere microorganisms for plant nutrition under changing climatic conditions. "Microbes can be our best allies" when it comes to promoting plant growth #PlantACT #HHU