Jaruwatana (Sodai) Lotharukpong

Heya science peeps, my first first-author paper is on Biorxiv! We show how transcriptome-wide expression variability in outbred animals responds massively to an environmental stressor and is underpinned by cryptic variability- (not just mean-) controlling alleles. www.biorxiv.org/content/10.6...

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.

Amazing! Do you think the scope for further developmental complexity is limited if a single Argonaute already does so many things?

Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that play central roles in gene regulation and developmental process...

One protein. One pathway. A whole germline fate.

New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...

🧵 Just out in Cell after more than 10 years in the making!

🎓 www.cell.com/cell/fulltex...

Plants and animals evolve radically different body plans.

Do they also operate under fundamentally different molecular evolutionary constraints during organ formation?

@cellpress.bsky.social

Genome editing in brown algae! 🧬🪸🌿 Now out in Cell Reports Methods!

Excited to share this highly efficient, transgene-free CRISPR–Cas genome editing protocol for brown algae, requiring no cloning and no specialized equipment.

doi.org/10.1016/j.cr...

#CRISPR #BrownAlgae
@mpi-bio-fml.bsky.social

GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner. Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond

DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/di...

Can we tune a plant’s epigenetic toolkit to disrupt plant homeostasis in ways that enable phenotypic innovation?

🌱Check out our new Opinion Paper with @thanvisrikant.bsky.social discussing this topic in @cp-trendsplantsci.bsky.social!

www.sciencedirect.com/science/arti...

Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model Stem cell–derived mesodermal organoids reveal how signaling centers guide cell fate and tissue organization.

🎉 Our deconstructed, stem-cell–based approach to studying signaling centers and limb-development cell types is out! 🥳 So nice to see it in its final form after the preprint— and huge thanks to the community for all the enthusiasm and interest since then!
www.science.org/doi/10.1126/...

To launch the start of the new recruitment round for PhD positions at the institute, we're highlighting this month one of our doctoral researchers for our #WeAreMPIBio #WeAreFML series: Jaruwatana Sodai Lotharukpong who joined IMPRS in 2021. Read about his work and interests: tinyurl.com/yeysnm8w

Pleased to be a small part of this molecular palaeobiology study by Jialin Wei, led by Marta Álvarez-Presas and Jordi Paps, with help from Davide Pisani. Animals repeatedly used similar genomic solutions to the challenges of terrestrialization @bristolpalaeo.bsky.social @bristolbiosci.bsky.social

NEW pub in @science.org 🥳

Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?

For over 15 years, #phylogenomic studies have been divided.

We provide new evidence suggesting that...

🔗: www.science.org/doi/10.1126/...

🚀 philentropy v0.10.0 is on CRAN!

Now with long-awaited parallel distance computation & a full speed-optimized refactor thanks to Andrew Gene Brown.
Compute 50+ distances/divergences in R faster than ever.

📦 CRAN: cran.r-project.org/web/packages...
💻 Code: github.com/drostlab/phi...

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

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...

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! 🎉

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

Reductive evolution of the DNA replication machinery in endosymbiotic fungi The molecular machinery for replicating and repairing DNA accurately is critically important for life and highly conserved across the Tree of Life. Here we show that two major lineages of fungi, Glome...

I’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵

doi.org/10.1101/2025...

A thread 👇

The entire "canvas" for the regulatory genome is surprisingly distinct in brown algae and the evolution of this chromatin landscape *happens* 🤔👽👾 to coincide with the independent origin of complex multicellularity. A lot of food for thoughts!!

Rewiring of chromatin regulation underlies the evolution of brown algal multicellularity Chromatin structure plays a central role in regulating transcription, genome stability, and epigenetic inheritance in eukaryotes. Much of our understanding of chromatin architecture and histone post-t...

Super glad to contribute to this study on chromatin evolution in brown algae! Special thanks to Jeromine Vigneau, @borglab.bsky.social and Susana Coelho for making this happen.

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

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

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

ggplot2 4.0.0 A new major version of ggplot2 has been released on CRAN. Find out what is new here.

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...

How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...

Mechanical forces drive evolutionary change A small tissue fold present in fruit fly embryos buffers mechanical stresses and may have evolved in response to mechanical forces.

Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social ‬ & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

Conservation of bilaterian genome structure is the exception, not the rule - Genome Biology Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although no...

Delighted to share the peer-reviewed version of our study led by @tomlewin.bsky.social now out in Genome Biology @bmc.springernature.com! We analyzed 64 chromosome-level genomes across 15 animal phyla and found that extensive genome rearrangements are the norm in bilaterians.
doi.org/10.1186/s130...

And of course, kudos to the authors for generating improved chromosome-level genome assemblies/scaffolding for brown algae that will be an important resource of the brown algal field!

Wondering how general the genomic patterns observed in animals are for multicellular organisms across the eukaryotic tree of life! 🧬🪾🤔

The application of irreversible genomic states to define and trace ancient cell type homologies - EvoDevo Homology, or relationship among characters by common descent, has been notoriously difficult to assess for many morphological features, and cell types in particular. The ontogenetic origin of morpholo...

The diversity of brown algae (tissue types, sexual systems, morphological "complexity", life cycle types) given the conserved macro-synteny reminds me of two interesting articles I recently read: link.springer.com/article/10.1... and link.springer.com/article/10.1...

A really cool study led by Josue and @agalip.bsky.social detailing the nature of sex chromosomes in brown algae, including the origin and repeated losses of U/V sexual systems. Brown algae also has highly conserved macro-synteny, retained at least ~224 Ma!! Interesting gene age data too!