Clustering the protein universe of life using DIAMOND DeepClust - Nature Methods DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...

DIAMOND DeepClust: an ultrafast clustering method for organizing the protein universe of life.

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

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity...

Out now in @newphyt.bsky.social with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social & more! Our high-quality pennycress pangenome is a striking example of genome architecture shaping different kinds of genomic variation, including some surprising centromeric movement

Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress Schultz et al. show that polar algae harbor extensive endogenous giant virus elements that are transcriptionally active, stress responsive, and integrated into host regulatory networks, highlighting v...

A good read on a large virus...

Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress: Current Biology www.cell.com/current-biol...

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...

Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below!
doi.org/10.1126/scie...

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.

Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9

What brown algae taught me about the importance of jumping genes for genome evolution

Behind the scenes!
go.nature.com/4bYY8BM

I love it! Amazing work

Our work on chromatin evolution in brown algae is finally out!

This is also my first "co-first author" paper!! I’m excited to share what we found 👇

Does hidden protein biology live in the suboptimal alignment space?

When we align two divergent proteins, we usually trust a single optimal alignment. 🧬

But what if the real structural signal lies in the space of near-optimal solutions?

With EMERALD-UI you can unfold this perspective.

📣 Meet the new ERC Synergy Grant awardees!

Sixty-six research teams have been selected for funding, bringing together 239 scientists. Congratulations to all!

➡️ buff.ly/PSn3bi9

#EUfunded #HorizonEurope #ERCSyG

This Halloween, we have a spooky evolutionary story for you.
The brainchild of @delaconcepcionjc.bsky.social, Nick Irwin and our fantastic collaborators is now out in @natplants.nature.com www.nature.com/articles/s41...
Here’s why I love this work — and why I think you’ll enjoy it too. 👇

A comparative analysis of transposable element diversity and evolution across 75 bee genomes - BMC Genomics Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

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

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...

Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella Auxenochlorella, green algae shaped by evolutionary forces acting on vegetative diploids, are amenable to discovery research and bioengineering via efficie

Excited to introduce Auxenochlorella as a new algal reference organism for fundamental plant science and bioengineering. A paper in two parts: a genetic toolkit for site-specific genomic manipulation, paired with the most unusual genome I’ve ever worked on

academic.oup.com/plcell/artic...

A mosaic of modular variation at a single gene underpins convergent plumage coloration The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and ...

1/9 New in @science.org www.science.org/doi/10.1126/science.ado8005
How does genetic architecture constrain evolutionary trajectories? To address this question, we inferred the genetic architecture of convergent plumage coloration and its evolutionary history in wheatears.

3/9 The black-or-white throat polymorphism is explained by the interaction of a transposable element (an LTR retrotransposon) upstream ASIP with ASIP coding variation. Mantle and neck side coloration is encoded by additive effects of regulatory variants upstream ASIP.

We discovered an endogenous retrovirus that's still spreading in natural D. melanogaster populations! It was horizontally transferred from D. erecta in Central Africa, so we named it "Kuruka", which means "jump" in Swahili. Read its cool story here: www.biorxiv.org/content/10.1...

Thrilled to share what we learned from re-annotating the mobilome of the brown algae model [Ectocarpus] 🌊🌿🏖️

genomebiology.biomedcentral.com/articles/10....

A wonderful collaboration with @ericadinatale.bsky.social, @cssmartinho.bsky.social, @rorycraig.bsky.social, and Susana Coelho! 🎉

It would be exciting to study whether there are clear "causal" links between TE regulation and body plan formation in brown algae, where 'artificial' mobilisation of young TEs can drive innovation (and overcome constraints) in the formation of multicellular phenotypes.

Thank you!!

Thank you Vangeli!

Huge thanks to Susana Coelho, @hajkdrost.bsky.social, @cssmartinho.bsky.social and @rorycraig.bsky.social for their guidance and support throughout this massive work!

5/5 🔮 Brown algae are a unique lineage in the tree of life, and working on them gave me a new perspective on the diversity of TE landscapes and regulation mechanisms across eukaryotes!

4/5 ✨ And my favourite part: intact TEs are preferentially associated with small RNAs and with the histone modification H3K79me2. Their interplay offers a curious insight into alternative regulatory strategies.

3/5 🧬 Over 80% of genes contain at least one intronic TE insertion. These intronic elements are shorter and more degraded than intergenic TEs, and overall they show minimal impact on gene expression.

2/5 🧜 TEs form discrete, repeat-rich islands that don’t correspond to centromeres. We also found an interesting enrichment in the pseudo-autosomal region of the sex chromosome, likely fueled by local hopping of DNA transposons from the sex-determining region.

1/5 🌊 The Ectocarpus genome harbors a high diversity of evolutionarily young TEs. DNA transposons dominate, but Gypsy elements carrying a Tudor domain caught our eye!