sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong
@sodail.bsky.social
140 followers 250 following 9 posts
ꙩ ꙫ ө ꚛ ꙮ ༗ :: complex multicellularity in brown algae :: doctoral researcher :: max planck institute for biology :: tübingen https://lotharukpongjs.github.io/
lotharukpongjs.github.io
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hajkdrost.bsky.social
Hajk-Georg Drost @hajkdrost.bsky.social · 6d
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...
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Reposted by Jaruwatana (Sodai) Lotharukpong
hajkdrost.bsky.social
Hajk-Georg Drost @hajkdrost.bsky.social · 6d
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! 🎉
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Reposted by Jaruwatana (Sodai) Lotharukpong
ericadinatale.bsky.social
Erica Dinatale @ericadinatale.bsky.social · 7d
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
alexdallaire.bsky.social
Alexandra Dallaire @alexdallaire.bsky.social · Sep 3
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
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · 19d
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!!
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · 19d
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
natmethods.nature.com
Nature Methods @natmethods.nature.com · 20d
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
thomasp85.com
Thomas Lin Pedersen @thomasp85.com · 27d
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
charlottewright.bsky.social
Charlotte Wright @charlottewright.bsky.social · 27d
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
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mpi-cbg.de
Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · Sep 3
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
jermp.bsky.social
Giulio Ermanno Pibiri @jermp.bsky.social · Aug 28
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
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Reposted by Jaruwatana (Sodai) Lotharukpong
yjluo.bsky.social
Yi-Jyun Luo @yjluo.bsky.social · Aug 18
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
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · Aug 25
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!
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · Aug 25
Wondering how general the genomic patterns observed in animals are for multicellular organisms across the eukaryotic tree of life! 🧬🪾🤔
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · Aug 25
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...
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...
link.springer.com
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · Aug 25
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!
natecoevo.nature.com
Nature Ecology & Evolution @natecoevo.nature.com · Aug 25
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
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ferdix.bsky.social
Ferdinand Marlétaz @ferdix.bsky.social · Aug 13
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
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sodail.bsky.social
Jaruwatana (Sodai) Lotharukpong @sodail.bsky.social · May 10
Congrats 🎉🎉 and what a beautiful graphical abstract!
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cedricfeschotte.bsky.social
Cedric Feschotte @cedricfeschotte.bsky.social · Apr 30
💥🥳 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
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ianakim.bsky.social
Iana V. Kim @ianakim.bsky.social · May 7
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
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Reposted by Jaruwatana (Sodai) Lotharukpong
Heng Li @lh3lh3.bsky.social · Apr 18
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
www.biorxiv.org
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Reposted by Jaruwatana (Sodai) Lotharukpong
giacomogattoni.bsky.social
Giacomo Gattoni @giacomogattoni.bsky.social · Apr 24
New preprint from my PhD in @amphispacelab.bsky.social is out! 🥳

We investigated the evolution of my favorite gene FoxQ2 across 21 animal phyla, and found three ancient paralogs with a very dynamic history.

More on phylogeny, synteny, and comparative in situs in the 🧵 below!

tinyurl.com/2j96px45
Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs
FoxQ2 is a highly conserved class of Forkhead-box transcription factors expressed on the anterior side of the body in cnidarians and bilaterians. Despite this conserved expression pattern, recent phyl...
tinyurl.com
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thibautbrunet.bsky.social
Thibaut Brunet @thibautbrunet.bsky.social · Apr 3
Striking new study from @archaeon-alex.bsky.social's lab just out in @science.org on multicellular development induced by compression in Archaea: www.science.org/doi/10.1126/...
Tissue-like multicellular development triggered by mechanical compression in archaea
The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...
www.science.org
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mayavoichek.bsky.social
Maya Voichek @mayavoichek.bsky.social · Mar 17
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte
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wcratcliff.bsky.social
Will Ratcliff @wcratcliff.bsky.social · Mar 19
1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics.

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