AMAPEC v1.0
AMAPEC is a machine learning framework developed in the Thomma lab to predict antimicrobial activity in fungal secreted effector proteins.
Antimicrobial Proteins in Lichen Symbioses
Lichens are complex symbiotic systems in which fungi interact not only with photosynthetic partners, but also with diverse microbial communities. We investigate how antimicrobial proteins (AMPs) help lichen-forming fungi establish and maintain these associations.
Peltigera rufescens growing in Cologne (Picture taken by Ciaran Kelly).
Our research focuses on the lichen genera Umbilicaria, which contain green algae as photosynthetic partner, and Peltigera, which contain cyanobacteria as photosynthetic partner, and which harbor remarkably diverse AMP repertoires. Recent chromosome-scale genomic analyses of Peltigera revealed extensive expansions of AMP-encoding genes, many of which are located in rapidly evolving, transposable element-rich regions of the genome. Transcriptomic analyses further showed that these genes are actively expressed within the lichen thallus.
AMP repertoire composition and conservation in Peltigera mycobionts (figure taken from Joisten-Rosenthal et al. 2026).
Intriguingly, the genomic organization of AMP genes in Peltigera resembles patterns previously observed in fungal pathogens, suggesting that mutualistic and pathogenic fungi may share common molecular strategies for interacting with other organisms. We hypothesize that AMPs enable lichen-forming fungi to shape their associated microbiomes, suppress unwanted microbes, and maintain stable symbiotic partnerships.
By combining comparative genomics, evolutionary biology, and functional studies, we aim to uncover how AMPs contribute to the ecology and evolution of lichen symbioses.
Variable Starship-like elements occur across 41 Peltigera genomes and colocalize with transposable elements (TEs; figure taken from Joisten-Rosenthal et al. 2026)).
In collaboration with junior group AG Rövenich, we also investigate how Verticillium can engage in interactions with green algae. We focus on the Verticillium side of such interactions while AG Rövenich investigates how green algae perceive, respond to, and interact with this fungus.
Algal cells physically attach to fungal hyphae.
Most relevant literature
Joisten-Rosenthal et al. (2026). A chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungi. BioRxiv doi:10.64898/2026.06.16.732702
Mesny et al. (2026). Plant-associated fungi co-opt ancient antimicrobials for host manipulation. Sci Adv. 12: eaec1406.
Mesny F et al (2024). Meddling with the microbiota: Fungal tricks to infect plant hosts. Curr Opin Plant Biol. 82: 102622.
Snelders NC et al. (2022). Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev. 46: fuac022.