Andrea Doddi

Evolutionary mechanisms underlying bacterial adaptation to the plant environment Abstract. Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that

Evolutionary mechanisms underlying bacterial adaptation to the plant environment

in @femsjournals.bsky.social Microbiology Reviews by @zakisaati.bsky.social et al

academic.oup.com/femsre/advan...

Pls RT‼️ @hanhtkvu.bsky.social lab @embl.org & we @cosheidelberg.bsky.social are looking for a #postdoc to study #regeneration x #autophagy across kingdoms of life.
www.health-life-sciences.de/opportunitie... Pls spread the word & get in touch if you are interested.

This one has been a long time in the making. So many contributions and years of hard work went into bringing this project to the finish line. I’m really happy to finally share our new story. Thanks to everyone involved, and a very special thanks to @teamthomma.bsky.social and @lfaino.bsky.social

🎉 Yesterday we enjoyed the glorious defence of @gabriellapetti.bsky.social of her @unicologne.bsky.social PhD thesis on "Homologous antimicrobial proteins in plants and fungi: conserved mechanisms shaping the plant microbiota" #proudPI #PhDone ..mind the crown modeled after the Ave1 NMR structure!😍

📢 Three new #bioRxiv preprints from our team on holocentric chromosomes.

Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇

Facultative heterochromatin mediated by core and accessory chromosome-encoded H3K27-specific methyltransferases controls virulence in a fungal phytopathogen Abstract. In many fungal phytopathogens, infection is regulated by accessory genomic regions enriched in facultative heterochromatin, but the precise role

Beyond excited to see this work finally out in @narjournal.bsky.social! We show that epigenetic modifiers on fungal accessory chromosomes can contribute to the overall epigenetic profile. Many thanks to @gomezlucia93.bsky.social and our other amazing collaborators 👏🏻

academic.oup.com/nar/article/...

We have a new preprint!
In this study, we use #genomic data to uncover population structure and adaptive potential in the meadow #spittlebug, the main European #vector of #Xylella fastidiosa.

📣 Major milestone achieved! First @teamthomma.bsky.social @unicologne.bsky.social PhD student graduated 🎉! Congratulations to @wolki95.bsky.social for a stellar defence of a thesis on antimicrobial effectors of Verticillium dahliae that drive niche adaptation #proudPI #PhDone

starbase: A Database and Toolkit for Exploration of Extremely Large Mobile Elements in Fungi https://www.biorxiv.org/content/10.64898/2025.12.04.686951v1

The biodiversity, genomics, ecology and evolution of mushroom-forming fungi - Nature Reviews Biodiversity Mushroom-forming fungi have along evolutionary history and a suite of important ecological roles. This Review highlights advances in understanding of Agaricomycetes evolution and ecology driven by gen...

Everything you always wanted to know about mushroom-forming fungi! Great collab with amazing mycologists. Thanks Laszlo Nagy for leading this effort!

www.nature.com/articles/s44...

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...

Florigen activation complex forms via multifaceted assembly in Arabidopsis - Nature In flowering plants, DNA–FD–14-3-3 recruits FT to the florigen activation complex both through DNA–FT interactions and by reducing liquid phase condensation of FD protein, which promotes dimerization,...

📣Paper alert! New paper out in @nature.com by the group of George Coupland @mpipz.bsky.social and colleagues on new roles for the florigen protein in flowering 🌱🌿. Congratulations!👏👏 👉https://www.mpipz.mpg.de/pr-coupland-2025-11-en
#Arabidopsis #plantsci
www.nature.com/articles/s41...

Very proud and happy to have contributed to this work. Special thanks to @antonkraege.bsky.social, @wolki95.bsky.social and @teamthomma.bsky.social

Differential contributions of an antimicrobial effector from Verticillium dahliae to virulence and tomato microbiota assembly across natural soils https://www.biorxiv.org/content/10.1101/2025.09.30.679524v1

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

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

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

Last week, our latest @biorxivpreprint.bsky.social preprint was released, a joint-venture of @antonkraege.bsky.social & @wolki95.bsky.social and co-directed by @nicksnelders.bsky.social a 🧵

Undermining the cry for help: The phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria https://www.biorxiv.org/content/10.1101/2025.06.09.658588v1

Congrats Lara!!

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 community...

Curious about my PhD research @parkergroup.bsky.social? The paper is available as preprint on bioRxiv now!
🔬 The interaction between scopoletin and fungal endophyte F80 rescues plant growth under iron-limiting conditions by resolving the iron mobility bottleneck.
📝 www.biorxiv.org/content/10.1...

Exploring the untapped potential of single‐cell and spatial omics in plant biology Advances in single-cell and spatial omics technologies have revolutionised biology by revealing the diverse molecular states of individual cells and their spatial organization within tissues. The fie...

Excited to share my new Tansley Review @newphyt.bsky.social on emerging single-cell and spatial omics technologies, many of which are just beginning to be applied in plant biology! Big opportunities lie ahead for the field. [1/n] 

nph.onlinelibrary.wiley.com/doi/10.1111/...

🌿We are thrilled to share that Prof. Miltos Tsiantis @mpipz.bsky.social has been elected as new Fellow of the @royalsociety.org in recognition to his work on plant organ development 🌿🥳 🎉Congratulations! 👏👏 👉 bit.ly/435gPjT #plantsci

Vacancy — PhD Candidate Plant-pathogenic Fungus Interaction Are you an early-career researcher with a passion for molecular plant or microbial science? Would you like to take on a highly relevant project in the field of plant-pathogen interactions? Then we hav...

Are you interested in molecular plant microbe interactions and would like to study effector biology in Fusarium-lettuce patho-system? Consider this PhD position @uva.nl in the lab of Martijn Rep as part of our recently funded joint TKI project werkenbij.uva.nl/en/vacancies...

Giant transposons promote strain heterogeneity in a major fungal pathogen | mBio No “one size fits all” option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for d...

We dive into the dynamics of #starships 🚀 in a fungal pathogen to ask: how might these giant #transposons impact human health? We find they drive genome-wide variation, encode clinically-relevant traits and even transpose within the same strain! 🍄🧪 out today in mBio #goteam doi.org/10.1128/mbio...

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies aff...

Excited to share our latest preprint 🥳
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen
@danielcroll.bsky.social
#TESky
www.biorxiv.org/content/10.1...

A gnotobiotic system reveals multifunctional effector roles in plant-fungal pathogen dynamics Plants host diverse microbiota that influence physiological processes and can enhance resilience against invading pathogens that, in turn, evolved effector proteins to manipulate host microbiota in th...

Last week, our newest @biorxiv-plants.bsky.social‬ preprint saw the light, led by @wolki95.bsky.social and co-directed by Kathrin Wippel (SILS, Amsterdam): A gnotobiotic system reveals multifunctional effector roles in plant-fungal pathogen dynamics www.biorxiv.org/content/10.1...

A gnotobiotic system reveals multifunctional effector roles in plant-fungal pathogen dynamics https://www.biorxiv.org/content/10.1101/2025.03.27.645772v1

Apoplastic barriers are essential for nodule formation and nitrogen fixation in Lotus japonicus Establishment of the apoplastic root barrier known as the Casparian strip occurs early in root development. In legumes, this area overlaps with nitrogen-fixing nodule formation, which raises the possi...

Finally!
Im so excited to present to culmination of many years of work from the fantastic Defeng Shen and some great collaborators. For details, I have made a digested thread below, but if you are more interested feel free to reach out (and read the paper of course).
www.science.org/doi/10.1126/...

Time to move on!

Heading to Zürich🇨🇭 where I will join the group of @mvanderheijden.bsky.social for my second post-doc.

I am very thankful for my time with @teamthomma.bsky.social at the University of Cologne. I learned a lot and cannot wait to share more of our findings soon.

So long Köln…

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae. Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, are enriched in virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. We further uncover extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, we demonstrate how Starship activity facilitated the de novo formation of a novel virulence gene. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence. ### Competing Interest Statement The authors have declared no competing interest.

📣New year, new preprint @biorxiv-microbiol.bsky.social 🎉! A study led by the brilliant @yukiyosato.bsky.social showing that Starship giant transposons dominate plastic genomic regions in the fungal plant pathogen Verticillium dahliae and drive virulence evolution. 🧵[1/12] doi.org/10.1101/2025...