Yu Sugihara

Check out our latest work on the discovery and engineering of PiggyBac transposases! 🧵

Accurate and efficient phylogenetic inference through end-to-end deep learning https://www.biorxiv.org/content/10.1101/2025.09.30.679045v1

Low mutation rate but high male-bias in the germline of a short-lived opossum Abstract. Age and sex have been found to be important determinants of the mutation rate per generation in mammals, but the mechanisms underlying these fact

New paper led by @yadirapga.bsky.social!

Opossums have babies at 6-months of age, but are still highly male-biased in their mutations

academic.oup.com/genetics/adv...

We discovered a new family of c-di-NMP receptors, widespread in bacteria & regulating🦠motility @pnas.org

A great collab. w/ @mygalperin.bsky.social @vikramalva.bsky.social @thethormannden.bsky.social

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

@hhu.de @cmfi.bsky.social
@sfb1381.bsky.social
@mibinet.bsky.social

JXB EDITORIAL INTERNSHIPS 2026 Who is this for? • Early career researchers (2-8 yrs postgrad/postdoc experience) What will you do? • Assess submitted manuscripts (with editorial mentorship) • Write commentary articles for publication in JXB • (Optional) Join JXB's social media activities Benefits for you: • Gain editorial & publishing experience • Career development as a researcher • Free SEB membership (1 year) • Invitation to JXB's Editorial Board meeting in 2026 Apply by 30th September 2025 bit.ly/jxbinterns

🚨 Applications are open for the 2026 JXB Editorial Internships! 🚨

🌱 Designed for ECRs, you will gain behind-the-scenes publishing experience, write commentary pieces & join the JXB Editorial Board meeting next year 👩‍💻✈️

Deadline: 30 Sept 2025

👉 bit.ly/jxbinterns

#PlantScience 🧪

📢 A Junior Professorship (W1, tenure track) is open at the Center for Plant Molecular Biology at Uni Tübingen (@zmbp-tuebingen.bsky.social) — to work on plant protein biochemistry (composition, structure, dynamics, or regulation of protein complexes). 🌱 Great opportunity — Apply by Oct 17th!

BIK1-RIN4 complex links plant immunity and pathogen virulence Plants deploy receptor-like cytoplasmic kinases (RLCKs) and the immune hub protein RIN4 to coordinate PAMPs-triggered immunity (PTI). Here, we show that BIK1, but not its close homolog PBL1, dynamical...

BIK1-RIN4 complex links plant immunity and pathogen virulence

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

Super excited and honoured to have been awarded an ERC Starting Grant for CooPAIRation!

How do plant immune receptors work together to trigger an immune response? Can we modulate immune responses for disease resistance? We will tackle these questions in CooPAIRation

Positions to be announced soon!

Systematic discovery and engineering of synthetic immune receptors in plants Plants deploy a diverse array of pattern recognition receptors (PRRs), which perceive microbe-associated molecular patterns to activate immune responses. Leucine-rich repeat receptor-like kinase subgr...

Very happy to share our latest work “Systematic discovery and engineering of synthetic immune receptors in plants” out in @science.org !

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

Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.

Learn more abt projects: cxli233.github.io/cxLi_lab/res...

Check out our new pre-print! ✨
We cloned AvrWTK4, the first wheat powdery mildew effector recognised by a tandem kinase protein, and show that an HMA-like integrated domain in WTK4 acts as pathogen decoy. Discover the whole story on bioRxiv ⬇️

Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations. #BLAST #Visualization #Genomics #Bioinformatics #BMCbioinformatics
bmcbioinformatics.biomedcentral.com/articles/10....

Why do speciation rates vary across the tree of life?
Some of the best yet most underappreciated places for this investigation are natural hybrid zones.
This preprint takes you to the hybrid zones in the origin of species to find a clue. 👉 shorturl.at/N7FXE
#Speciation #Evolution #hybridization

🚨 New publication by the research group of @dessimoz.bsky.social @unil.bsky.social @sib.swiss in @natecoevo.nature.com 👇

Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur

So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...

How sex shapes transcriptome evolution in the songbird brain Sex differences have captivated scientists for a long time, yet the evolutionary rate of change in sex-biased gene expression has not been directly quantified. To address this issue, we leverage brain...

I'm a little bit late, but happy to see this new paper led by @imillercrews.bsky.social and anchored by @rosvall-lab.bsky.social now out on bioRxiv.

We analyze comparative songbird RNA-seq data using new features in our software package, CAGEE. Check it out!

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

Two major breakthroughs for the nucleotide immune signaling field in pre-print by @romihadary.bsky.social @soreklab.bsky.social www.biorxiv.org/content/10.1...

(1) Beautiful bioinformatic analyses reveal known viral nucleotide sponges are members of enormous protein families ubiquitous in phages

Rēs ipSAE loquunt: What’s wrong with AlphaFold’s ipTM score and how to fix it AlphaFold’s ipTM metric is used to predict the accuracy of structural predictions of protein-protein interactions (PPIs) and the probability that two proteins interact. Many AF2/AF3 users have experie...

Here' the ipSAE githubd and preprint:

github.com/DunbrackLab/...
www.biorxiv.org/content/10.1...

Friday Flower 001: Mimulus lewisii 🌸✨

Monkeyflowers are masterpieces of design with nectar-guide spots formed by an activator–inhibitor system of MYB transcription factors. These generate reaction–diffusion patterns across the ventral petal.

Inbreeding reduces fitness in spatially structured populations of a threatened rattlesnake | PNAS Small and fragmented populations are at high risk of local extinction, in part because of elevated inbreeding and subsequent inbreeding depression....

www.pnas.org/doi/full/10....

The MUC19 gene: An evolutionary history of recurrent introgression and natural selection We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants ...

Our paper on the evolution of MUC19 in humans, Neanderthals, and Denisovans is finally out today in Science!

This has been a six-year effort by 13 authors to weave together 3 separate but related evolutionary stories around this one gene (more on thread 🧵).

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

Plant-associated fungi co-opt ancient antimicrobials for host manipulation Evolutionary histories of effector proteins secreted by fungal pathogens to mediate plant colonization remain largely elusive. While most functionally characterized effectors modulate plant immunity, ...

📣 NEW PREPRINT 📝

We identified evolutionary origins of many fungal effectors!
We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression.
www.biorxiv.org/content/10.1...

cc @teamthomma.bsky.social

How can we better understand the plant immune system? In my new @cp-cellhostmicrobe.bsky.social piece, I propose “immune cell states” as a framework for uniting molecular and cellular perspectives.

www.cell.com/cell-host-mi...

Rewinding the tape: historical contingency and functional constraints have shaped the evolution of APikL virulence effectors in the blast fungus Protein evolution is influenced by historical contingencies and functional constraints, but their combined impact on rapidly diversifying pathogen virulence effectors remains poorly understood. Here, ...

We’re excited to share our latest work on plant pathogen effector protein evolution @biorxivpreprint.bsky.social. With @kamounlab.bsky.social and Abbas Maqbool.

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

Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out!

Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).

www.nature.com/articles/s41...

Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages Abstract. Plant domestication is sometimes associated with a reduction in the diversity of immune receptor genes, critical for pathogen recognition and def

Bourne et al. analyzed immune receptor gene repertoires of 15 domesticated crop species, showing that grapes, mandarins, rice, barley, and yellow sarson exhibit reduced immune receptor gene repertoires compared to wild counterparts.

🔗 doi.org/10.1093/gbe/evaf147

#genome #evolution #PlantSky

Group leader (m/f/d) | Plant Development and Diversity The successful applicant will be expected to build an independent research group to study plant development and/or its natural variation.

Junior #GroupLeader position @mpipz.bsky.social
on Plant Development & Diversity ‼️ #plantsci www.mpipz.mpg.de/5697690/job_...

Phyling: phylogenetic inference from annotated genomes Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...

This looks like an amazing tool
www.biorxiv.org/content/10.1...

Group Leader position available @johninnescentre.bsky.social !

It’s a creative and stimulating environment for plant and/or microbial biology - spanning the full spectrum of fundamental and applied research.

Apply to join us - don’t be shy!

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...