Yu Sugihara

Model: Activation and suppression of defences in plant–aphid interactions. Upper left panel: aphid stylet penetration of the cell wall releases oligogalacturonides (OGs), which induce PAMP/DAMP-triggered immunity (PTI/DTI) in a process dependent on BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1 (BAK1), ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), and CPK5/6/11 (data herein). The stabilisation of pattern recognition receptors (PRRs) and coreceptors at the plasma membrane may rely on the deubiquitination (DUB) activity of ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSHs; Gravino et al., 2024). Upper right panel: the Mp10 effector, introduced by aphids into the cell cytoplasm (Mugford et al., 2016), suppresses OG-induced reactive oxygen species (ROS) (data herein) and flg22-induced PTI (Bos et al., 2010). Mp10 targeting of plant AMSHs is implicated in these processes (Gravino et al., 2024). EDS1 is essential for Mp10-mediated ROS suppression and PRR destabilisation (data herein), acting through an unidentified mechanism (denoted by the double-sided arrow with an asterisk). Lower left panel: effector-triggered immunity (ETI) is activated through EDS1, either directly or indirectly, upon recognition of Mp10 and/or its activities by a TNL (Gravino et al., 2024; Rao et al., 2024). Salicylic acid glucosyltransferase 1 (SGT1) is also required for TNL/ETI activation (Bos et al., 2010). Lower right panel: aphids secrete additional effectors, such as cathepsin B proteins (e.g. CathB6), which target EDS1 to suppress ETI (Liu et al., 2025). Solid arrows, increased activation; solid blunt-ended arrows, increased suppression; Dashed arrows, reduced activation; Dashed -blunt-ended arrows, reduced suppression.

🎉Thrilled to share our latest work, now published in @newphyt.bsky.social!

🧑‍🔬 @matteogravino.bsky.social, @samtmugford.bsky.social, @saskiahogenhout.bsky.social et al., @johninnescentre.bsky.social

#️⃣ #PlantScience #PlantImmunity

📄 Read the full paper👇
nph.onlinelibrary.wiley.com/share/8QSRJ9...

Srsly @newphyt.bsky.social ???

A conserved stripe rust effector elicits variable resistance responses in wheat Plant resistance (R) and pathogen avirulence (Avr) gene interactions are central to pathogen recognition and disease resistance in crops. However, functional characterisation of Avr effectors in Pucci...

Our first wheat stripe rust Avr effector story. It is a short one that points to suppressors in this pathosystem while we could not link this Avr effector to a described R gene. www.biorxiv.org/content/10.1...

How common is homoploid hybrid speciation? - PubMed Hybridization has long been considered a process that prevents divergence between species. In contrast to this historical view, an increasing number of empirical studies claim to show evidence for hyb...

Good question! My go-to guide is this classic from @mollyschumer.bsky.social et al:
pubmed.ncbi.nlm.nih.gov/24620775/

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab.

Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.

#plantscience
www.biorxiv.org/content/10.1...

Ancient hybridization underlies tuberization and radiation of the potato lineage Genomic and functional analyses reveal that the potato lineage originated from a homoploid interspecific hybridization event between the Tomato and Etuberosum lineages 8–9 million years ago. The alter...

The hybrid origin of potato tuberization.

From: www.cell.com/cell/fulltex...

Ancient hybridization underlies tuberization and radiation of the potato lineage Genomic and functional analyses reveal that the potato lineage originated from a homoploid interspecific hybridization event between the Tomato and Etuberosum lineages 8–9 million years ago. The alternate inheritance of highly divergent parental alleles drove the origin of tubers and explosive species diversification and niche expansion into the high Andes.

Now online! Ancient hybridization underlies tuberization and radiation of the potato lineage

Coalescence and Translation: A Language Model for Population Genetics Probabilistic models such as the sequentially Markovian coalescent (SMC) have long provided a powerful framework for population genetic inference, enabling reconstruction of demographic history and an...

Cool new paper on pop gen and machine learning:

www.biorxiv.org/content/10.1...

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Happy to share that our Helixer deeplearning-based annotation of 230 superasterid genomes is now online on
@datadryad.bsky.social
💻🌱

doi.org/10.5061/drya...

Check out how we used 69 of them to study the molecular evolution of a plant immune receptor network here! 👇

ASTER: A Package for Large-scale Phylogenomic Reconstructions. #Phylogenomics #SpeciesTreeInference @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/advance-...

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...

Independent Fellowship in Plant-Associated Microbial Interactions | John Innes Centre An exciting opportunity for an Independent Fellowship in Plant-Associated Microbial Interactions has arisen at the John Innes Centre. To read the full job description for this role…

Exciting opportunities to establish your group at JIC! Come join our vibrant research community in Norwich!

🔹 Independent Fellowship in Plant-Associated Microbial Interactions (path to tenure-track)
tinyurl.com/yk576jms
🔹 GL in Discovery Plant Sciences (tenure-track or tenured)
tinyurl.com/mwbs4dhn

JIC GROUP LEADER VACANCY

We're looking for interests in areas including, but not limited to, growth and development, environmental and organism interactions, physiology, signalling and molecular processes, taking quantitative cell biological, genetic, biochemical and modelling approaches.

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

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

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Model of Starship mediated transfer of the ToxA gene, that is present on a separate mobile element named ToxhAT. Blue: ToxhAT; Green: Starship Horizon; Yellow: Starship Sanctuary.

Curious about how novel #plant #pathogens emerge? Check out our microreview on whether #fungal disease outbreaks are instigated by Starship #transposons. We present three examples that we think are evidence of outbreaks caused by Starship HGT. bsppjournals.onlinelibrary.wiley.com/doi/10.1111/...

I’m very grateful and excited to start our ARIA-funded project on redesigning plant immunity!

First Ma lab #GMI paper is now online! It‘s a mini-review on insect-induced plant #galls —their coolness and research potential! Plant galls induced by insects: Coordinated developmental reprogramming and defence manipulation www.sciencedirect.com/science/arti...

The evolution of suppressed recombination between sex chromosomes and the lengths of evolutionary strata Abstract. The idea that sex-differences in selection drive the evolution of suppressed recombination between sex chromosomes is well-developed in populatio

academic.oup.com/evolut/advan...

Aphid effectors suppress plant immunity via recruiting defense proteins to processing bodies Aphids hijack plant immunity via p-bodies, but plants fight back with a heat shock protein in an unexpected twist on defense.

Our paper is now online in Science Advances! Congrats @saskiahogenhout.bsky.social @johninnescentre.bsky.social and all coauthors!
www.science.org/doi/10.1126/...

In #GENETICS, @3rdreviewer.bsky.social‬ and @smishra677.bsky.social‬ show it is possible to estimate recombination solely using the allele frequency spectrum and provide a genealogical interpretation of the results, showing how #MachineLearning can provide insights into biology.

buff.ly/emixz9W

Very happy to finally present my poster to a very interested audience! It’s always a pleasure to discuss about agro, commonly seen as a tool, but still a (cool) plant pathogen. Still at #2025ISMPMI, so if you are interested in my work, don’t be shy to say hi!

Group Leader in Discovery Plant Sciences | John Innes Centre The John Innes Centre (JIC) seeks a visionary Group Leader to lead research on Discovery Plant Science.

GROUP LEADER VACANCY

JIC is recruiting a Group Leader in Discovery Plant Sciences.

If you think your research would synergise and thrive at JIC, please apply.

www.jic.ac.uk/vacancies/gr...

Thank you to AmirAli Toghani @amiralito.bsky.social, Raoul Frijters, Tolga Bozkurt @tolgaboz.bsky.social, Ryohei Terauchi, and Sophien Kamoun @kamounlab.bsky.social for the wonderful supports!

🎉 Exciting news during #2025ISMPMI
Our AlphaFold sensor vs helper NLR paper is now published in @newphyt.bsky.social‬!

Big thanks to the reviewers for their constructive feedback 🙏

📖 Check out the peer-reviewed version here 👇
🔗 nph.onlinelibrary.wiley.com/doi/10.1111/...

bsky.app/profile/yusu...

GitHub - DanielleMStevens/mamp-ml: mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2 mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2 - DanielleMStevens/mamp-ml

While there's lots of work to be done, mamp-ml is a critical advancement in plant immunology for accelerating receptor-epitope characterization and engineering resistance. Mamp-ml is on Github and we implemented a version on Google Colab for easy use. Please check it out!
github.com/DanielleMSte...

mamp-ml: A deep learning approach to epitope immunogenicity in plants Eukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...

#2025ISMPMI 📣 In silico screening of PRR-epitope interactions is now possible!

Here, we developed mamp-ml to predict their immunogenic outcomes without structural context. Let's accelerate engineering plant receptors for robust resistance! 🚀🌱 Small 🧵

www.biorxiv.org/content/10.1...

Excited to attend my 1st ISMPMI conference, and present our work on a paired wheat CNL/MLKL receptor mechanism! 🌾

Come chat to me at my poster on Tuesday, P-050! 📜

If you miss my poster session, I will be talking in: Crop resistance genetics and genomics on Wednesday - 16:25-16:35!