Fabian van Beveren

Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts Author summary Cytoplasmic incompatibility (CI) is a reproductive strategy used by certain bacteria to promote their spread within arthropod populations. These bacteria, inherited through the mother, ...

Diversity and spread of #cytoplasmicIncompatibility genes among maternally inherited #symbionts

#SymbioSky

doi.org/10.1371/jour...

Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur

So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...

New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.

onlinelibrary.wiley.com/doi/epdf/10....

I gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.

The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats

No, AlphaFold has not completely solved protein folding Biology is hard. Yes, even for AI.

AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...

Microbe with bizarrely tiny genome may be evolving into a virus With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses

𝗠𝗶𝗰𝗿𝗼𝗯𝗲 𝘄𝗶𝘁𝗵 𝗯𝗶𝘇𝗮𝗿𝗿𝗲𝗹𝘆 𝘁𝗶𝗻𝘆 𝗴𝗲𝗻𝗼𝗺𝗲 𝗺𝗮𝘆 𝗯𝗲 𝗲𝘃𝗼𝗹𝘃𝗶𝗻𝗴 𝗶𝗻𝘁𝗼 𝗮 𝘃𝗶𝗿𝘂𝘀
or maybe not. a 🧵

roland @environmicrobio.bsky.social‬ ‪and Krzysztof @ktjurdzinski.bsky.social‬ already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls - Nature Plants New fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution, providing a comprehensive database that underscores the ancient divergen...

A fantastic resource for fern biology @natplants.nature.com 🔽!

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

Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽

www.biorxiv.org/content/10.1...

Sounds very cool, excited to have a look!

Angomonas deanei with flourescent-labeled nucleus and endosymbiont. ETP9 localizes at the endosymbiont division site.

Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...

Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity Land plants include angiosperms, bryophytes, lycophytes and ferns, each of which may deploy distinct strategies to resist pathogens. Here, we investigate fern-pathogen interactions by characterizing n...

🔗 Preprint alert: www.biorxiv.org/content/10.1...

🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿

Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]

Similar to these ECM plants, I also adapted to new symbiotic partners at the @lrsv-toulouse.bsky.social and I’m happy we’ve been able to do cool science together! 🙌

In our study, the included ECM-only species have retained most of these genes, but what role they play in different ECM lineages remains an open question!

For the full story, see our letter in @newphyt.bsky.social!

(5/5)

The Ectomycorrhizal Fungus Laccaria bicolor Produces Lipochitooligosaccharides and Uses the Common Symbiosis Pathway to Colonize Populus Roots The ectomycorrhizal fungus Laccaria bicolor produces lipochitooligosaccharides that activate nuclear calcium spiking in its Populus host and then uses the

Some ECM plants lost the ability to do any intracellular symbiosis, such as arbuscular mycorrhizal (AM) symbiosis. Yet, certain genes involved in AM symbiosis play a symbiotic role in ECM-only plants (e.g. doi.org/10.1105/tpc...., doi.org/10.1111/nph....).

(4/5)

Phylogeny of rosids showing the genome completeness and symbiotic status of each species. On the right of the tree, presence/absence is shown for a variety of genes. On the left of the tree, duplications of specific gene families are shown in a set of nodes representing multiple ectomycorrhizal and non-ectomycorrhizal lineages.

Using comparative genomics, we find more evidence for these independent origins. We detected several genes that are convergently duplicated in different ECM lineages. Several of these are related to cell wall remodeling, which can be important for symbiosis!

(3/5)

Phylogeny of rosid species. Ectomycorrhizal status is shown for all species, including estimations for this trait for all nodes in the phylogeny.

Many plants form mutualistic relationships with ectomycorrhizal (ECM) fungi  – fungi that enter the root but stay extracellular. Even in just the rosids, 17 different ECM plant lineages are known. We reconstructed their evolution and found that ECM symbiosis originated at least 16 times.

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Ectomycorrhizal symbiosis evolved independently and by convergent gene duplication in rosid lineages Click on the article title to read more.

Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054

With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social

A thread: (1/5)

Postdoc Comparative genomics and genome architecture in early-diverging fungi and their protist relatives (3-year position)

Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...

Super interview sur @franceculture.fr de @chloe-beaulieu.bsky.social, sur nos travaux publiés dans @naturegenet.bsky.social !

www.radiofrance.fr/francecultur...

Hello Bluesky!

Follow us for updates on our Microbiology research here @w-u-r.bsky.social