The two papers: www.science.org/doi/10.1126/...

and

www.science.org/doi/10.1126/...

Weisberg Lab PhD student Boluwatife Giwa presented her research on Botrytis genomics at the 2026 APS Pacific Division Meeting and was awarded the 1st place poster award and a travel award. Congrats!

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us

Here is it! Super new science from us on horizontal gene transfer & bact defense systems! Liyana OW YONG discovered the first-of-its-kind defense factor AbjA that triggers 'abortive conjugation' as a defense mechanism, by targeting the T4SS! How neat?! #MicroSky 1/7

www.biorxiv.org/content/10.6...

A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth.

Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. http://dlvr.it/TRWtVp ☄️

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

Final version of our last paper is out!
www.nature.com/articles/s41...

Effector-triggered stomatal immunity prevents leaf invasion by bacterial pathogens www.biorxiv.org/content/10.64898/2026.03...

What this technology is going to do is not end higher education, but it is going to undo so much of the baseline work on accessibility by pushing overworked professors to take things back to offline modalities, in person timed exams, keeping tech out of the classroom, etc.

Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!

Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...

USDA postdoctoral fellowships are open. If you’re interested in writing a postdoc fellowship with me in plant immunity, spatial defense, or vector-borne disease, please reach out.
(US citizens, nationals, permanent residents only; PhD awarded Jan 2023–Jan 2027.) www.nifa.usda.gov/grants/progr...

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

Excited to share that PNAS published our research article focused on "Why are Ralstonia goofy?"

This position is still open. The Weisberg lab is recruiting a postdoc or Ph.D. student to study horizontal gene transfer in plant-associated microbial communities. Please see the job ad for more information and feel free to contact me if you have any questions!

Three male side-blotched lizard with three neck colors: orange, blue, and yellow

Lizards have evolved their own version of rock-paper-scissors. Here's my story on the genetics behind nature's games. Gift link: nyti.ms/493KGMI

Identifying Effective Cryoprotectant Agents for Emerging Bacterial Model Species Host-associated bacteria live amongst eukaryotes within varied niches and form relationships ranging from facultative to obligate. With advancement in studies of such symbiotic associations, fastidiou...

After years of struggling with how to cryopreserve one of our endosymbiotic bacteria, we found something that worked!
🦠☃️
We crowd-sourced suggestions and then @ruthwright.bsky.social tried the most common ones (like 🥛...). Want to do the same? Here is how we did it:
www.biorxiv.org/content/10.6...

Cell wall patterning regulates plant stem cell dynamics The plant cell wall regulates development through spatiotemporal modulation of its chemical and mechanical properties. Pectin methylesterification is recognized as a rheological switch controlling wal...

Thrilled to have our paper out in @science.org. Cell division guides plant cell wall formation. Does the reverse hold? We show that bimodal pectin methylesterification, via PME5 mRNA nuclear sequestration, influences plant cell division and cell plate orientation. www.science.org/doi/10.1126/...

A wheat resistosome defines common principles of immune receptor channels - Nature Evolutionary conservation of plant receptor structure allowed for generation of new variants of wheat and barley nucleotide-binding leucine-rich repeat receptors (NLRs) that recognize AvrSr35 of the w...

"Common principles of immune receptor channels..." #ThingsThatMakeYouGoHmm 🤔 www.nature.com/articles/s41...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

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How does the arms race between #bacterial defense systems and mobile genetic elements contribute to #microbiome community structure?

Read below for an insightful exploration of this issue! It will not disappoint
@plosbiology.org 🧪
#bacteria #immune #phage #ecology

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

New preprint: 🚀🧬 Starship in the genome of the lichen fungus Xanthoria. Discovery of giant transposons Starships challenged what we thought we knew about fungal genomes. But what about Starships in #lichen fungi? Let us present Tangerine! 🖥️ 🧪 🦠 🧫 #SymbioSky doi.org/10.1101/2025...

Cellular energy sensor SnRK1 suppresses salicylic acid–dependent and –independent defenses and bacterial resistance in Arabidopsis | PNAS In nature, plants cope with various pathogens that compete for cellular resources during infection. It has long been suggested that plant defense a...

Cellular energy sensor SnRK1 suppresses salicylic acid–dependent and –independent defenses and bacterial resistance in Arabidopsis

www.pnas.org/doi/abs/10.1...

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

I tried an even harder example on Gemini Pro image generation and this is quite scary/amazing. I asked for a microscopy image of around 20 HeLa cells, GFP tagged 20% nuclear, 10% membrane, +1 nuclear staining, + overlap. Image below and prompt in the following post.

Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.

tinyurl.com/5yx2wmz5

(1/n)

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...