Yu Sugihara

Fungal genome sequencing for free! 👇🏼 #GGFungi2026

#GGFungi2026 Call For Projects is now open for applications getgenome.net/callforproje...

We will be holding an information session today 3rd March at 14:00 CET (08:00 Eastern US; 18:00 PKT). To sign up please complete this short form - forms.office.com/e/DssYYkkY9Z

There is a week left to apply for two available positions in my lab @ipbhalle.bsky.social

- PhD: ipb-halle.mhm.jobs/12-phd-posit...

- Postdoc: ipb-halle.mhm.jobs/13-postdocto...
Earliest start date: 01/05/2026.

We are interested in plant immune receptor biochemistry and evolution. Please share!

Computational design of sequence-specific DNA-binding proteins - Nature Structural & Molecular Biology The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammali...

This paper is great. It describes a method to generate DNA binding proteins de novo: www.nature.com/articles/s41...

I wish there is a web server where you can punch in DNA sequences, submit a job, then it generates the cDNA of your DNA binders, and you can go straight for synthesis & testing.

GitHub - Gaius-Augustus/Tiberius: Tiberius is a deep learning gene finder. Tiberius is a deep learning gene finder. Contribute to Gaius-Augustus/Tiberius development by creating an account on GitHub.

What we more recently learnt about Tiberius: the models trained on softmasked genomes are very sensitive to how the genome was masked for inference. It seems safer to use models trained on unmasked genomes. #genomeannotation #geneprediction github.com/Gaius-August...

Fig. 7 Newly annotated PHAS loci are associated with Kronos-specific genomic variations.

✨ Paper spotlight ✨

(🧵1/6) The annotated blueprint: Integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv. Kronos
nph.onlinelibrary.wiley.com/doi/10.1111/...

#PlantScience

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

Join us on March 10, 2026 at Kyoto University 🇯🇵 for a day celebrating my long-time friend and collaborator Prof. Ryohei Terauchi.

"Kyoto Mini-Symposium on Plant–Microbe Interactions"

RNA splicing generates a functionally specialized Rep protein isoform in geminiviruses — enabling timely control of the viral cycle. Strikingly, similar strategies might have evolved in DNA viruses infecting different kingdoms: www.biorxiv.org/content/10.6... Spearheaded by @delphinem-p.bsky.social!

It’s that time of year! #SchoBozKa in Downing College, Cambridge 🇬🇧

Running strong since 2017–Annual lab meeting of the teams of Sebastian Schornack, Lida Derevnina, Phil Carella, Jiorgos Kourelis and Sophien Kamoun.

This year’s guest is Steven Spoel, University of Edinburgh

Fig. 1 Pik pairs as resources for determining optimal ‘chassis’ for engineering recognition.

Mismatch screening in Nicotiana benthamiana to explore Pik-1/Pik-2 paired NLR platforms for receptor engineering

A #Letter by Xi & Banfield
👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue

Two independent origins of XY sex chromosomes in Asparagus Abstract. The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enables the investigation of molecular dyna

@pbentz.bsky.social @scarey.bsky.social @jleebensmack.bsky.social et al. explore the origins of recombination suppression between ancestral autosomes leading to independent sex chromosome formation in Asparagus.

🔗 doi.org/10.1093/molbev/msag003

#evobio #molbio #PlantSky

How specific are heritable symbioses?

And what can we learn from swapping obligate symbionts across host species?

We address this in our latest, led by @inespons.bsky.social & in our collaboration w/ @microbiome.bsky.social 🦠🪲 Out today in @natcomms.nature.com!

1/n
www.nature.com/articles/s41...

📣 Our latest story just dropped on bioRxiv:: A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts www.biorxiv.org/content/10.6... 🧵

Structural basis for the broad recognition specificity of an Arabidopsis immune receptor https://www.biorxiv.org/content/10.64898/2026.02.04.703898v1

Benthamiana rhapsody 🎶 🌱

How benthi is the go-to system for cracking the activation mechanism of an Arabidopsis TIR-NLR immune receptor— that’s the rhapsody.

Congrats He Zhao and Selvaraj for this wonderful collaboration 👇🏼 doi.org/10.64898/202...

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

This is a beautiful case of how real science happens & serious scientists work. Kudos to both set of authors: “This has been a humbling experience, but one that speaks to the self-correcting nature of the scientific endeavor.” www.science.org/doi/10.1126/...

Structural basis of canonical TIR-NLR activation in plant innate immunity https://www.biorxiv.org/content/10.64898/2026.02.03.703613v1

Fig. 2 (shortened, full legend in paper): Structurally characterized M. oryzae effectors in complex with the HMA or HMA-like domains of host target proteins and ID-NLRs. Crystal structures of (A) AVR-PikF with the HMA-like domain of OsHIPP19 from rice (7B1I) (Maidment et al., 2021); (B) APikL2A with the HMA-like domain of sHMA25 from foxtail millet (7NLJ) (Bentham et al., 2021); (C) Pwl2 with the HMA domain of OsHIPP43 from rice (8R7D) (Zdrzałek et al., 2024); (D) AVR-PikD with the HMA-like ID of Pikp-1 from rice (5A6W) (Maqbool et al., 2015); (E) AVR-Pia with the HMA-like ID of Pikp-1 (6Q76) (Varden et al., 2019); (F) AVR1-CO39 with the HMA-like ID of RGA5 from rice (5ZNG) (Guo et al., 2018). Complexes are displayed such that the HMA/HMA-like domains are in equivalent orientations. Domains from HPP/HIPP host targets are coloured light green. Domains from ID-NLRs are coloured dark green.

⚙️🦠 REVIEW 🦠⚙️

Turley & Faulkner explore the function of plant heavy metal-associated domain-containing proteins and speculate about their functions at plasmodesmata by drawing from plant–pathogen interaction studies.

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪 Christine Faulkner

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

Please share!
My group at @zmbp-tuebingen.bsky.social is offering a post-doctoral position (4 years). We look for a structural biologist with experience in Cryo-EM/Cryo-ET to investigate the mechanisms of host invasion by pathogenic fungi. Deadline February 28th!
uni-tuebingen.de/universitaet...

1/12 I'm ecstatic to share my preprint on legume NLR tissue expression! We investigated the NLRomes of 28 legumes + 4 outgroups, examining tissue expression across 7 legume species. Paper thread below 🧵👇
@thesainsburylab.bsky.social @itqbnova.bsky.social
🔗https://doi.org/10.64898/2026.01.25.701577

Got my PhD yesterday! Had a great discussion during my viva and I'm truly grateful for the support from my supervisors + examiners + friends and peers at TSL. Where I am today has been shaped by all of you — and exciting journeys ahead! 🎓✨

New paper with @smishra677.bsky.social!

How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.

1/

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

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...

Why I’m genetically engineering a rainbow flower…

And how a Russian fairy tale inspired the idea 🧵

Botanical Triumph in a 16th Century Italian Villa YouTube video by Linnean Society

You can also enjoy Paola Bonfante's wonderful Linnean Society lecture "Botanical Triumph in a 16th Century Italian Villa" youtu.be/nKwA9xK-oGg?...

The splice of life: how alternative splicing shapes regulatory and phenotypic evolution - The EMBO Journal Alternative splicing (AS) is a key mechanism for generating regulatory and phenotypic diversity in multicellular eukaryotes. Large-scale comparative transcriptomic studies have revealed that AS leads ...

"In this review, we highlight the patterns and mechanisms of AS evolution across species, exploring how technological advancements are transforming our understanding of splicing evolution"

link.springer.com/article/10.1...

Fig. 1 Pik pairs as resources for determining optimal ‘chassis’ for engineering recognition.

✨ Paper spotlight ✨

(🧵 1/7) Mismatch screening in Nicotiana benthamiana to explore Pik-1/Pik-2 paired NLR platforms for receptor engineering
nph.onlinelibrary.wiley.com/doi/10.1111/...