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/
https://lotharukpongjs.github.io/
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...
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
🚀 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...
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...
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.
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
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.
genzplyr is dplyr, but bussin fr fr no cap.
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...
www.nature.com/articles/s41...
October 2, 2025 at 9:06 AM
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...
www.nature.com/articles/s41...
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! 🎉
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
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! 🎉
genomebiology.biomedcentral.com/articles/10....
A wonderful collaboration with @ericadinatale.bsky.social, @cssmartinho.bsky.social, @rorycraig.bsky.social, and Susana Coelho! 🎉
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
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
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
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:
rdcu.be/eITQH
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 👇
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
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 👇
doi.org/10.1101/2025...
A thread 👇
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...
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
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...
www.biorxiv.org/content/10.1...
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...
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
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...
www.nature.com/articles/s41...
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
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...
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
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...
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...
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
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...
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...
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
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...
www.biorxiv.org/content/10.1...
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...
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
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...
doi.org/10.1186/s130...
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...
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
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!
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
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
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
with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
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 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
💥🥳 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 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
Reposted by Jaruwatana (Sodai) Lotharukpong
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
May 7, 2025 at 3:23 PM
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...
Reposted by Jaruwatana (Sodai) Lotharukpong
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
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Jaruwatana (Sodai) Lotharukpong
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
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
April 24, 2025 at 3:11 PM
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
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
Reposted by Jaruwatana (Sodai) Lotharukpong
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
April 3, 2025 at 6:24 PM
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/...
Reposted by Jaruwatana (Sodai) Lotharukpong
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 🧵👇
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 🧵👇
March 17, 2025 at 11:56 AM
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 🧵👇
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 🧵👇
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
www.nature.com/articles/s41...
March 19, 2025 at 7:18 PM
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...
www.nature.com/articles/s41...
Reposted by Jaruwatana (Sodai) Lotharukpong
1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genome duplication in a long-term multicellularity evolution experiment - Nature
In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...
www.nature.com
March 5, 2025 at 11:00 PM
1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jaruwatana (Sodai) Lotharukpong
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...
[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...
How do ancient genes regulate animal embryo development at single cell resolution | University of Dundee, UK
A PhD project at the University of Dundee
www.dundee.ac.uk
March 3, 2025 at 11:44 AM
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...
[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...
Reposted by Jaruwatana (Sodai) Lotharukpong
Another @biorxiv-evobio.bsky.social preprint of work led by @wenfeixian.bsky.social. With our Lausanne colleagues, we revisit the Napoleon Oak. An earlier long-read genome had revealed a relatively low number of somatic mutations (www.nature.com/articles/s41...).
1/2
1/2
Low number of fixed somatic mutations in a long-lived oak tree - Nature Plants
Sequencing of nested branches from a 234-year-old oak tree reveals a low number of somatic mutations accumulating during its lifetime, implying that mechanisms are in place to reduce these potentially...
www.nature.com
February 16, 2025 at 2:48 PM
Another @biorxiv-evobio.bsky.social preprint of work led by @wenfeixian.bsky.social. With our Lausanne colleagues, we revisit the Napoleon Oak. An earlier long-read genome had revealed a relatively low number of somatic mutations (www.nature.com/articles/s41...).
1/2
1/2