Fantin Mesny

A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insects

Various phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genes

Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.

Pleased to finally share this fun collab that began at #Ento23

@cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun).

Horizontal transfer of an #AntimicrobialPeptide across insects
bit.ly/DrsHGT

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Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

Deconstructing host quality offers insight into disease ecology Disease risk varies among ecological communities because species differ in their host quality, that is, their contribution to parasite fitness. We propose a four-component framework of host quality that harmonizes terminology across plant and animal domains. Using this framework, we demonstrate how the host defense strategies of resistance and tolerance relate to distinct components of host quality. Easily extendable to multi-parasite systems, the framework also helps to identify new ways of examining the continuum between specialist and generalist parasites. Ultimately, breaking down and formalizing the components of host quality helps with synthesizing disease ecology across domains and unlocking relationships between biodiversity and disease risk.

Online now: Deconstructing host quality offers insight into disease ecology

More than half of researchers now use AI for peer review — often against guidance A survey of 1,600 academics found that more than 50% have used artificial-intelligence tools while peer reviewing manuscripts.

Just decline the peer review invitation.

What are you people even doing?

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...

The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis ### Competing Interest Statement The authors have declared no competing interest. Agriculture and Agri-Food Canada, https://ror.org/051dzs374 Alberta Grain Saskatchewan Wheat Development Commissio...

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...

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....

Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria During pathogen attack, plants recruit beneficial microbes in a ‘cry for help’ to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonisation through vario...

📣 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....

Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

Why are there so few pathogens? Ecology and evolution in pathogen emergence Why are there so few pathogens, and what determines their emergence? This Perspective argues that ecological and evolutionary forces (host availability, geographic exposure and microbial innovation) w...

Given the tremendous diversity of microorganisms in the world, why do only a small fraction cause disease?

My essay in #PLOSBiology argues that the answer is lack of opportunity and that humans encounter only one new bacterial pathogen for every 1.4b years lived.

journals.plos.org/plosbiology/...

Could humans and AI one day form a single “evolutionary individual”? Researchers at the Max Planck Institute for Evolutionary Biology raise this question in a new publication exploring human–AI interdependence.
www.evolbio.mpg.de/3836073/news...

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health The human gut microbiome plays an important biological role in host health, yet over 60% of gut species remain uncultured and hence inaccessible to experimental manipulation. Here we analysed 11,115 h...

🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...

One mother for two species via obligate cross-species cloning in ants - Nature In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

Reproduction in ants 🐜 just keeps blowing my mind 🤯

But this here is the crown for sure... for now.

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

(go also check out obligate chimerism, social chromosomes, clonal production of females and males, and much more...)

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

Cooperation between a root fungal endophyte and host‐derived coumarin scopoletin mediates Arabidopsis iron nutrition Iron acquisition is a critical challenge for plants, especially in iron-deficient soils. Recent research underscores the importance of root-exuded coumarins in modulating the root microbiome communi.....

Super excited to share that my PhD research paper is finally out!
@newphyt.bsky.social

doi.org/10.1111/nph....

@parkergroup.bsky.social

Protein structure alignment significance is often exaggerated Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...

📣 Massively proud of this ⬇️ great study, led by the brilliant @mesny.bsky.social surprisingly uncovering that many pathogen effectors stem from ancient antimicrobials 🤯 #EffectorWisdom #EvoMPMI

Thanks a lot Ren! Happy you like it.

It was nice to see you at MPMI ☺️too bad we did not have the opportunity to talk more.

Many thanks to @teamthomma.bsky.social for inspiring discussions and to all co-authors for their important contributions: @alvalentinawolf.bsky.social, @antonkraege.bsky.social, @wolki95.bsky.social, @jinyi-zhu.bsky.social, @yukiyosato.bsky.social and others not on @bsky.app.

So, many effectors have ancestral antimicrobial properties. These were retained over evolution while host manipulation traits evolved. Today, they can still function to antagonize competitors and, thus, they have dual functions.

Are the antimicrobial properties still relevant? Using a gnotobiotic system, we show that the Vd424Y effector contributes to colonization in presence of a plant-associated microbiota.

One of the 5 effectors, Vd424Y, carries a nuclear localization signal necessary for immunomodulation in planta. The NLS was only acquired recently. Thus, plant-colonizing fungi repurposed antimicrobials to suppress host immunity.

Strikingly, among most conserved antimicrobials, many effectors previously shown to manipulate plant immunity occurred. We selected 5 and all of them antagonized microbial growth in vitro!

The broad conservation of fungal antimicrobials suggests ancient origins. Of course, fungi roamed the earth and competed with other microbes before land plants or animals existed. Ancient weapons worth keeping during evolution?

With AMAPEC, we now analyzed phylogenetically diverse fungi with divergent lifestyles and found that fungi secrete lots of antimicrobials. Interestingly, quite some are widely conserved throughout the Fungal Kingdom.

First challenge: how to find novel fungal antimicrobial effectors. To do so, we developed AMAPEC, an accurate predictor of antimicrobial activity tailored to fungal effectors.
More info and links ⬇ bsky.app/profile/team...

Fungal effectors are mainly seen as pathogen-secreted proteins that mediate plant colonization by manipulating host physiology (immunity). Recently, some were shown to be antimicrobial & manipulate plant microbiota during infection.
State of the art in this review ⬇ bsky.app/profile/mesn...

Plant-associated fungi co-opt ancient antimicrobials for host manipulation Evolutionary histories of effector proteins secreted by fungal pathogens to mediate plant colonization remain largely elusive. While most functionally characterized effectors modulate plant immunity, ...

📣 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

The broad conservation of fungal antimicrobials suggests ancient origins. Of course, fungi roamed the earth and competed with other microbes before land plants or animals existed. Ancient weapons worth keeping during evolution?

With AMAPEC, we now analyzed phylogenetically diverse fungi with divergent lifestyles and found that fungi secrete lots of antimicrobials. Interestingly, quite some are widely conserved throughout the Fungal Kingdom.