Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵

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.

Last year, our collaboration effort with @sodail.bsky.social and Susana Coelho highlighted that Brown Algae are a promising model system to study the evolution of multicellularity and emergence of embryogenesis as a constrained developmental process shaping body plans.
www.nature.com/articles/s41...

Due to the curious nature of the [Ectocarpus] genome to select for young and potentially active TEs (majority DNA TEs), we did not manage to focus more on the retrotransposon biology of brown algae. Potentially active retrotransposons could be found with LTRpred:

joss.theoj.org/papers/10.21...

Our main findings:
1) Ectocarpus mobiome retains mostly recent, evol. young transposons (TEs)
2) These primarily young TEs are regulated by small RNAs in absence of canonical DNA methylation
3) Particular TE enrichment along the sex chromosomes
4) Developmental regulation of TEs through small RNAs

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! 🎉

In memory of Jane Goodall, English primatologist and anthropologist and the world's foremost expert on chimpanzees. Take a look at her 1985 article published in #PhilTransB 'Conditions of innovative behaviour in primates': royalsocietypublishing.org/doi/10.1098/...

So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:

rdcu.be/eITQH

🚀 Jalview 2.11.5 is here!

New features include:
✅ Tree visualisation for enhanced protein secondary structure analysis
✅ Consensus colouring for alignments and subgroups
✅ Improved command line options for 3D structure visualisation

Plus, key bug fixes and performance improvements.

Hot damn

"The settlement is largest payout in the history of U.S. copyright cases. Anthropic will pay $3,000 per work to 500,000 authors."

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...

Chaetognaths have lost gene body methylation and shifted #5mC back to Transposable Elements. This reversion to the ancestral state is coupled with a simplification of DNMT3 architecture. We posit that trans-splicing might compensate.

It is an honour to have contributed to this 20y struggle ⛰️.

'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory

Out after peer review now, follow up from our 2019 pna-NLRome paper (which was based on enrichment and long-read sequencing). It is remarkable how much more can be learned with complete genome sequences. Next. pan-NLRome from hundreds of A. thaliana long-read genomes! Big thanks to the entire team!

Happy to be able to finally share our NLR pangenome paper, out now in CHM.

"Pangenomic context reveals the extent of intraspecific plant NLR evolution"

www.cell.com/cell-host-mi...

#plantscience #plantimmunity #pangenomes #science #nlr

Deadline was just extended to 30th March! :)

Kind reminder that if you would like to learn more about the fundamental principles of embryo formation, please apply for this PhD post by 21st March :)

Please spread the word🙏:

[PhD Position in Computational Evolutionary Transcriptomics]

If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...

I sometimes wonder what a world would look like in which each incremental post was 1% better or more considered than the previous.

Starting to populate yet another social network seams like a good way to test this for me personally. Happy to be here now :)