Jaruwatana (Sodai) Lotharukpong
sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong
@sodail.bsky.social
ꙩ ꙫ ө ꚛ ꙮ ༗ :: complex multicellularity in brown algae :: doctoral researcher :: max planck institute for biology :: tübingen
https://lotharukpongjs.github.io/
Reposted by Jaruwatana (Sodai) Lotharukpong
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/...
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...
www.pnas.org
January 30, 2026 at 9:14 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
🧵 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
January 7, 2026 at 11:50 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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
January 2, 2026 at 2:20 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
github.com
December 22, 2025 at 4:18 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
December 12, 2025 at 11:49 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
🎉 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/...
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.
www.science.org
December 2, 2025 at 9:15 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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
December 1, 2025 at 2:54 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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
November 13, 2025 at 3:13 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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/...
November 13, 2025 at 8:34 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
🚀 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...
November 4, 2025 at 9:31 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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.
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.
github.com
November 6, 2025 at 11:25 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
October 2, 2025 at 9:06 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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! 🎉
October 2, 2025 at 9:06 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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
Characterization of the transposable element landscape shaping the Ectocarpus genome | Genome Biology
rdcu.be
October 1, 2025 at 8:12 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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 👇
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...
doi.org
September 3, 2025 at 3:21 PM
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...
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...
www.biorxiv.org
September 19, 2025 at 7:02 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
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...
www.nature.com
September 18, 2025 at 8:09 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
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 ...
tinyurl.com
September 11, 2025 at 3:22 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
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.
www.mpi-cbg.de
September 3, 2025 at 3:26 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
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...
www.biorxiv.org
August 28, 2025 at 12:16 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
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...
doi.org
August 18, 2025 at 9:39 AM
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!
Genomes of brown algae with different sex determination systems show that U/V sex chromosomes evolved 450–224 million years ago and show remarkable conservation of genes within the sex-determining region, despite independent expansions of the sex locus in each lineage

www.nature.com/articles/s41...
Origin and evolutionary trajectories of brown algal sex chromosomes - Nature Ecology & Evolution
Genomes of nine brown algal species with different sex determination systems show that U/V sex chromosomes evolved 450–224 Ma and show remarkable conservation of genes within the sex-determining regio...
www.nature.com
August 25, 2025 at 9:23 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41...
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
The genomic origin of the unique chaetognath body plan - Nature
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ...
www.nature.com
August 13, 2025 at 4:38 PM
Reposted by Jaruwatana (Sodai) Lotharukpong
💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...
www.pnas.org
April 30, 2025 at 10:45 AM