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Yu Sugihara

@yusugihara.bsky.social
410 followers 576 following 18 posts

Researcher at The Sainsbury Laboratory, Evolution | Population genetics | Plant-microbe interactions yusugihara.github.io

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Reposted by Yu Sugihara
Sebastian Schornack @dromius.bsky.social · 09/10/2026
How do "friendly" rhizobia build a legume nodule? @albinteulet.bsky.social found that Type III effectors of symbiotic Rhizobia include diverse predicted transcriptional and post-transcriptional modulators. journals.plos.org/plosbiology/... Now @plosbiology.org More information below.
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PLOS Biology @plosbiology.org · 09/10/2026
Symbiotic #rhizobia form nitrogen-fixing partnerships with #plant roots. This study by @albinteulet.bsky.social & @dromius.bsky.social uses structural modelling to predict how secreted proteins may mimic plant factors in a strategy shared with pathogens. 🧪 #AcademicSky #symbiosis plos.io/4j6bWj0
Network-based identification of structural units (SUs) present in multiple Nop effectors.
(A) Structural similarity network of the 96 structural units (SU) extracted from AlphaFold models of the 33 Nop effectors. Each node represents one region, and edges connect pairs of regions that are structurally similar with a TM-score above 0.5. Coloured circles delimit the 13 communities containing at least two members (SU1–SU13). The remaining grey nodes correspond to the 9 singleton units. (B–N) Overlays of all structural regions belonging to each community (SU1–SU13). The putative fold or function inferred from Foldseek analysis is indicated below each panel, with the number of occurrences in each community given in parentheses.
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juli g pausas @jgpausas.bsky.social · 09/10/2026
The new APG V has just been published @journalsysevo.bsky.social onlinelibrary.wiley.com/doi/full/10.... An updated classification of Angiosperms It includes a poster! www.tudelft.nl/en/hortus-bo... 🧪🌸🌳🌱🍁🌱🌴🌾🌿 #plantsci botany #plantbiology
Poster for the new Angiosperm Phylogeny Group (APG V) plant classification. It presents the current phylogenetic relationships among angiosperms, along with flower images representing all families
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 07/10/2026
A helper NLR monitors catalytic perturbation of a vesicle trafficking regulator targeted by pathogen effectors www.biorxiv.org/content/10.64898/20…
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Ziv Spiegelman @zivirus.bsky.social · 08/10/2026
Two NLRs, same viral effector, one pandemic. Happy to contribute to this study of a novel NLR against the ToBRFV movement protein 🍅
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Yu Sugihara @yusugihara.bsky.social · 08/10/2026
Excited to share our latest work! 🍅 Two evolutionarily distinct immune receptors recognize the same viral target, yet differ in their recognition spectra. A fascinating example of convergent evolution in plant immunity!
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
Together, our results point to convergent recognition of tobamovirus movement proteins by distantly related immune receptors. Their recognition ranges differ, and HREZ offers a complementary source of resistance to the pandemic virus. Preprint: www.biorxiv.org/content/10.6... (8/9)
biorxiv.org
Convergent recognition of tobamovirus movement proteins by phylogenetically distinct NLR immune receptors
The tobamovirus Tomato brown rugose fruit virus (ToBRFV) has rapidly emerged as a major threat to tomato production worldwide, overcoming the widely deployed Tm-22-mediated resistance and challenging ...
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
Does recognition lead to assembly? The four movement proteins recognized by HREZ—from TMV, ToBRFV, ToMV and PMMoV—also promoted formation of the large HREZ complex. For HREZ, recognition and immune complex assembly were tightly linked. (7/9)
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
But the two receptors are not interchangeable. Across movement proteins from eight related viruses, their recognition profiles overlapped but differed. Tm-2² recognized more of the panel, while HREZ strongly recognized the pandemic virus, ToBRFV. (6/9)
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
Then came the evolutionary surprise. HREZ and Tm-2² are not close relatives. They sit in distinct branches of the plant NLR immune receptor family. Yet both recognize tobamovirus movement proteins. Two evolutionary paths, one viral target. (5/9)
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
What happens after recognition? With ToBRFV MP present, HREZ assembled into a much larger protein complex. AlphaFold 3 modelling favoured a pentamer — five copies of HREZ assembled into a resistosome-like architecture. (4/9)
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
We tested three major ToBRFV proteins: the replication protein (RdRp), coat protein (CP) and movement protein (MP). Only MP triggered HREZ-dependent cell death in Nicotiana benthamiana. This provides direct evidence that ToBRFV MP activates HREZ. (3/9)
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Jogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026
🍅 Tomato brown rugose fruit virus spread worldwide. For >60 years, one resistance gene protected tomatoes. This virus broke through. A second gene confers resistance. The same viral target? Convergent evolution? Preprint: www.biorxiv.org/content/10.6... #EvoMPMI #NLRbiology (1/9) 🧵
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Sophien Kamoun @kamounlab.bsky.social · 07/10/2026
I just published: The night shift in the greenhouse A night-blooming cactus, a time-lapse, and the case for hosting artists in the lab. kamounlab.medium.com/the-night-sh...
kamounlab.medium.com
The night shift in the greenhouse
A night-blooming cactus, a time-lapse, and the case for hosting artists in the lab.
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Sophien Kamoun @kamounlab.bsky.social · 07/10/2026
Happening today! UPES Seminar Organizers
CGSB | New York University Abu Dhabi Speaker: Professor Sophien Kamoun, The Sainsbury Laboratory Title: Making Sense of the Alphabet Soup of NLR Immune Receptors Time: 4:00–5:00 p.m. UAE time docs.google.com/forms/d/e/1F...
docs.google.com
UAE Plant and Environment Society Sign-up
The UAE Plant and Environment Society (UPES) unites leading scientists, researchers, environmental advocates, and community members from across the Gulf to explore critical issues in plant biology, ec...
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phy_papers @phypapers.bsky.social · 07/10/2026
Convergent recognition of tobamovirus movement proteins by phylogenetically distinct NLR immune receptors www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 06/10/2026
Convergent recognition of tobamovirus movement proteins by phylogenetically distinct NLR immune receptors www.biorxiv.org/content/10.64898/20…
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 06/10/2026
Convergent recognition of tobamovirus movement proteins by phylogenetically distinct NLR immune receptors www.biorxiv.org/content/10.64898/20…
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Nick Desnoyer @nickdesnoyer.bsky.social · 05/10/2026
Montage of the Petunia lines I am currently growing 🌸 More on these in the podcast with @nikomccarty.bsky.social later this week!
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Charlotte Houldcroft @virologyhouldcroft.bsky.social · 04/10/2026
Fantastic outgoing third year Cambridge Genetics student Chris Leung has turned his prize-winning project on ARG methods for DNA viruses into a preprint www.biorxiv.org/content/10.6... @aylwyn-scally.bsky.social & I welcome your feedback.
biorxiv.org
Statistical inference of virus evolution using ancestral recombination graphs
Ancestral recombination graphs (ARGs) represent the coalescent history at every locus in the genome, subject to mutation and recombination. Modelling viruses using the coalescent with recombination re...
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Jenn Coughlan @jenncoughlan.bsky.social · 02/10/2026
I am delighted to share our new preprint, led by the amazing @stressedbranch.bsky.social! This paper was a real Herculean effort by four amazing postdocs across three labs and a small army of extremely talented undergraduates. www.biorxiv.org/content/10.6... 1/n
biorxiv.org
| bioRxiv
bioRxiv - the preprint server for biology, operated by openRxiv, a nonprofit organization dedicated to advancing scientific communication
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International Society for Molecular Plant-Microbe Interactions @ismpmi.bsky.social · 02/10/2026
Exciting News! Sophien Kamoun to give the Opening Keynote Lecture at the 2027 IS-MPMI Congress in Jeju Korea (18-22 July 2027). ismpmi.org/events/2027-...
ismpmi.org
2027 IS-MPMI Congress - IS-MPMI
Sophien Kamoun to give the opening keynote talk:                AI-Guided Studies of Plant Immunity Save the Date Sunday, 18 July – Thursday, 22 July Jeju, South Korea The 22nd International Congress ...
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Sophien Kamoun @kamounlab.bsky.social · 27/09/2026
I just published: How do we recognize world-class science? Not by the journal it appeared in What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs. kamounlab.medium.com/how-do-we-re...
kamounlab.medium.com
How do we recognize world-class science? Not by the journal it appeared in
What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs.
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Andrew Roger @andrewjroger.bsky.social · 18/03/2026
Finally, people should stop worrying about profile mixture models being over-parameterized for any sized dataset. It's not a valid concern. Please see: academic.oup.com/sysbio/artic...
academic.oup.com
Is Over-parameterization a Problem for Profile Mixture Models?
Abstract. Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process
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Andrew Roger @andrewjroger.bsky.social · 18/03/2026
So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.
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Nature @nature.com · 22/09/2026
Nature ersearch paper: Sex without crossovers mimics clonal reproduction in Rhynchospora tenuis go.nature.com/3UXKc6g
go.nature.com
Sex without crossovers mimics clonal reproduction in Rhynchospora tenuis - Nature
Rhynchospora tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis.
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Greger Larson @gregerlarson.bsky.social · 25/09/2026
I love how genomic analyses keep dismantling the concept that species cannot interbreed. Even better, ancient introgression often facilitates diversity in a domestic context. New paper shows this is in pigs too! www.science.org/doi/epdf/10.... A thrill to be a small part of a giant piggy effort!
science.org
Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs
Despite the ubiquity of wild boar populations across Eurasia, their origins, routes of dispersal, and phenotypic evolution remain uncertain. Here, using 745 genomes representing populations across Eur...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24/09/2026
AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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David Lowry @davidlowry.bsky.social · 24/09/2026
The monkeyflowers, including all those things we call Mimulus, have now been collapsed (along with some other small families) into the Orobanchaceae. This lumper couldn’t be happier. onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Large‐scale nuclear and plastid phylogenomic analyses inform an updated Angiosperm Phylogeny Group classification: APG V
We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of t...
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Josie Maidment @jmaidment.bsky.social · 25/09/2026
Happy to share that our study of the interaction between the MAX effector AVR-Pia and rice HMA domain-containing proteins has been published (as the cover article!) in PLOS Pathogens. journals.plos.org/plospathogen...
journals.plos.org
Two folds, many faces: The Magnaporthe oryzae MAX effector AVR-Pia targets novel rice HMA domain-containing proteins
Author summary Blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the world’s most devastating rice diseases. During infection, M. oryzae secretes a diverse set of molecules, known as ...
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Biophysical Journal @biophysj.bsky.social · 24/09/2026
#OPENACCESS: Proteome-wide structural and interaction analysis using cross-linking mass spectrometry and its applications. Shenbaga Moorthy Balakrishnan, Hifzur Rahman Ansari, and Taoufik Nedjadi. buff.ly/ovoTRNs
cell.com
Proteome-wide structural and interaction analysis using cross-linking mass spectrometry and its applications
Deciphering the mechanisms of protein-protein interactions (PPIs) and protein structural changes within the native cellular environment is crucial for advancing drug discovery. In vivo chemical…
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Molecular Biology and Evolution @molbioevol.bsky.social · 22/09/2026
Our new MBE Highlight focuses on the new study by @victoriaemullin.bsky.social et al. on the sharp decline in genetic diversity in Great Britain bumblebees. Museum collections reveal loss of genetic diversity in declining bumblebee populations 🔗 academic.oup.com/mbe/article/... #societyjournal
MBE Highlight: Museum collections reveal loss of genetic diversity in declining bumblebee populations
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David Hoey @davidjhoey.bsky.social · 16/09/2026
Introducing PhyloDig: a small command-line tool I am developing to make comparative phylogenetic analyses easier. github.com/davidjhoey/P...
github.com
GitHub - davidjhoey/PhyloDig: PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam d...
PhyloDig is a command line pipeline for automated homology mining across collections of protein and coding sequence databases. It combines HMMER searches, optional Pfam domain filtering, and sequen...
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Ben Parker @ben-parker.bsky.social · 21/09/2026
Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...
pnas.org
Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont | PNAS
Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 21/09/2026
A predicted interaction may involve only a small region of a protein complex. How can we identify confidence in that local interface when the surrounding regions have high PAE? Our tutorial uses a PAE matrix to explain how LIS can help 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AlphaFoldDB
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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Simon Snoeck @simonsnoeck.bsky.social · 18/09/2026
Complementary "CTNIP-SCREW-DEP/HSL3-NUT-DEPR" reads: 10.1016/j.molp.2025.10.005 (wheat) and 10.1016/j.xplc.2026.102074
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Tora Økland 🌱 @receptora.bsky.social · 16/09/2026
That's a wrap on #PPRM2026 ! Had a lot of fun with a community of researchers I really admire and appreciate, and was happy to have the chance to show what we work on. You can read the preprint on some of what I presented here: www.biorxiv.org/content/10.6...
biorxiv.org
Evolutionary diversification of the SymRK receptor family in land plants
Plant receptor-like kinases (RLKs) are involved in diverse processes, ranging from growth and reproduction to interactions with microbes. Variation in the extracellular domains delineates several RLKs...
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Richard Sever @richardsever.bsky.social · 16/09/2026
"eLife has been without an impact factor for just over a year...and [has] an overall 21% decrease in revenue" newsletter.journalology.com/p/journalolo... Perhaps the only more stark illustration of academia's addiction to Impact Factor is this:
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GetGenome @getgenome.bsky.social · 14/09/2026
Day 1 “AI in Genomics workshop” 🇹🇳 🌍 With thanks to @Googleorg @thesainsburylab.bsky.social @getgenome.bsky.social
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 13/09/2026
Ancestree: unified likelihood inference of ancestral alleles under supplied or inferred genealogies www.biorxiv.org/content/10.64898/20…
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Genetics Society of America @genetics-gsa.bsky.social · 15/09/2026
A comparative genomic analysis in #fungi with different morphologies of the septal pore cap identifies new genes underlying morphological convergence during fungal evolution. Find out more in the September issue of #G3journal 🔗 buff.ly/HMyZgcg
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Remco Stam @rstam.bsky.social · 11/09/2026
New preprint! There have been quite a few papers about RLP and RLK receptors, but none of them have a truly reproducible annotation pipeline (including my own...)... We finally made such a pipeline and look more systematically at RLPs within tomato. www.biorxiv.org/content/10.6...
biorxiv.org
PlantLRR-PRR:A Reproducible Annotation Pipeline Reveals Contrasting Evolution of Developmental and Defense Receptor-Like Proteins in Tomato
Plants perceive external and internal signals via receptors to modulate their growth, development, and defenses. Leucine-rich-repeat receptor-like-kinase (RLKs) and receptor-like-proteins (RLPs) are t...
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Andy Posbe @adnroide.bsky.social · 10/09/2026
Excited to share Fold on Tight! 🎉 We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond. 📝 zenodo.org/records/2210...
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Guavadk @guavadk.bsky.social · 09/09/2026
This project has been a labor of love and grateful for my supervisor @yusugihara.bsky.social’s guidance every step of the way 🌱🙏
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Guavadk @guavadk.bsky.social · 09/09/2026
🍄 We investigated conserved cytoplasmic effectors in Fusarium as targets for resistance breeding. Our harmonized annotation dataset for 305 Fusarium genomes is now on Zenodo. 📌 Poster: doi.org/10.5281/zenodo.22649574 📦 Dataset: doi.org/10.5281/zenodo.22224641 #PPATH2026
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Daniel Croll @danielcroll.bsky.social · 04/09/2026
Our lab is looking for PhD students to join us in 2027 🎓🎉 The projects can be structured around our research directions: - Transposable element dynamics - Fungal pangenomics - ML/language model genomics applications - Pathogen adaptation More here pathogen-genomics.org ("Jobs") and please share! 🙏
pathogen-genomics.org
Evolutionary genomics of pathogens
Croll lab at University of Neuchatel. The lab of Daniel Croll wants to understand how pathogens evolve to cause disease. For this, we mainly focus on major crop pathogens to unravel mechanisms of rapi...
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Edel Pérez-López 🇨🇦 @edelplopez.bsky.social · 04/09/2026
🚨 New paper out in @cp-cellrepsustain.bsky.social ! 🪲🌱 This work highlights the need for better biosurveillance and the promise of natural pest control 👏 Bravo Jordanne! 💚 Merci NSERC, RQRAD & the growers who have welcomed us onto their farms for six years! 🔗 www.cell.com/cell-reports...
graphical abstract showing leafhoppers and biocontrol
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