Yu Sugihara

Postdoctoral Researcher (Salem Group) | John Innes Centre An exciting opportunity has arisen for a Postdoctoral Researcher to join the newly appointed group of Dr Hassan Salem at the John Innes Centre, working on cutting-edge science in the field of Crop…

VACANCY - We’re looking for a Postdoctoral Researcher to join Dr @hassansalem.bsky.social group, in the field of Crop Genetics.

www.jic.ac.uk/vacancies/po...

Closing date - 15 December 2025
Salary - £37,500 - £45,350
Contract - Full-time, 17 months in the first instance (potential up to 4 yrs)

CC-NLRs exhibit diverse conformations in the resting state. Figure depicts different NLR resting and activated states. While ZAR1 exists as a monomer bound to its guardees in its resting state, several forms have been observed for the NRC2 helper, including dimers, tetramers, and filaments. While filament-like structures were observed via confocal microscopy for NRC2 upon overexpression in planta, these structures were not detected for its paralog NRC4, suggesting a potentially different resting state configuration for NRC4. Our work suggests that the Pik CC-NLR pair forms a hetero-complex bound to the plasma membrane in its resting state. How effector binding to the integrated domain (ID) of the Pik-1 sensor leads to the activation of the complex remains to be determined.

Excited to share our latest work on plant immune receptor biochemistry! @kamounlab.bsky.social @hsuanpai.bsky.social @mpcontreras.bsky.social Jose Salguero Linares @danielluedke.bsky.social @adnroide.bsky.social @jiorgoskourelis.bsky.social

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

Huge honor to receive this price! Glad to see the lichen research rewarded with such a distinction
Thanks @pierremarcdelaux.bsky.social and @kellerjeanphd.bsky.social for your SUPERvision ✨

Merci @academiesciences.bsky.social pour cette opportunité et cette belle cérémonie!

I have a new preprint demonstrating a genome-architecture-aware approach to inferring species trees and introgression landscapes from a small number of genomes. If you are interested in phylogenomics, birds, or hybridization, this is for you! www.biorxiv.org/content/10.1...

The Pik NLR pair accumulates at the plasma membrane as a hetero-oligomeric sensor-helper immune protein complex prior to activation https://www.biorxiv.org/content/10.64898/2025.11.30.691369v1

k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence doi.org/10.1186/s128...

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans Abstract. Haplotype-based statistics are widely used for finding genomic regions under positive selection. At the heart of many such statistics is the comp

Rahman, Smith & Szpiech present selscan v2.1, a dynamic programming algorithm to improve runtime and memory usage in the calculation of extended haplotype homozygosity.

🔗 doi.org/10.1093/molbev/msaf275

#evobio #molbio #compbio

A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen | mBio Sustainable food production requires the management of disease agents attacking crops. Application of antifungal compounds is among the key elements of pathogen containment; however, resistance can ri...

Finally out!
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...

A big thanks to @danielcroll.bsky.social & @GabrielScalliet

#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.

No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.

Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com

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

Some news 🎉
After five incredible years in Tübingen, it’s time to say goodbye.

Starting February, the Mutualisms Lab will relocate to the John Innes Centre, right next door to @berasymbionts.bsky.social and her group at The Sainsbury Laboratory 🪲🦠

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/...

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

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#PhageSky A bacterial long-term evolutionary tradeoff, dating as far as 200 years in the past.
Very proud to have a small contribution in this great work from Karasov & Burbano Labs led by @taliamycota.bsky.social & Jiajun Cui & Emma Caullireau. Please read the thread by @hernanaburbano.bsky.social:

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

Postdoctoral Researcher (Dr Miguel Montez) | John Innes Centre An exciting opportunity has arisen for a Postdoctoral Researcher to join the Wellcome Trust project led by Dr Miguel Montez and hosted within the Dodd Group at the John Innes Centre.

📣 Looking for a 3-Year Postdoc @johninnescentre.bsky.social to join my Wellcome project.

This is a highly interdisciplinary project that explores chromatin dynamics in 🌱 plant responses across timescales, from circadian rhythms to seasonal changes

📅 Closes on 10 Dec.
www.jic.ac.uk/vacancies/36...

A Banner that shows the open call for the international PhD program on interdisciplinary Plant Biology in Cologne Germany between University of Cologne and Max Planck Institute for Plant Breeding Research. A button reads "apply now!".

We’re #hiring! Our #IMPRS @mpipz.bsky.social & @unicologne.bsky.social recruits 4 PhD students. We look for candidates with a keen interest in experimental & computational plant biology to join us in 2026!

Find details at www.mpipz.mpg.de/imprs/imprs-... and apply by Jan 5.

#PlantSciJobs

NEW pub in @science.org 🥳

Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?

For over 15 years, #phylogenomic studies have been divided.

We provide new evidence suggesting that...

🔗: www.science.org/doi/10.1126/...

the top half shows two panels with microscopy images. Left is a light-microscopy image of a group of algal cells. The cells are round with different sizes. Two arrows point at sporangia: one looks as if someone stuffed 8 footballs in a thin elastic bag. The other is perfectly round and contains many small spores within. The right panel shows the same group of cells, but in fluorescent microscopy, where green color shows chloroplasts. In each cell the chloroplasts are globular with small lobes sticking out. The bottom half shows a photo of Xanthoria lichen - bright yellow and leafy growing on a tree branch

Our paper on the #genome of the Trebouxia #photobiont from Xanthoria is now out in @newphyt.bsky.social! Check below for a near-chromosome level assembly, secretome analysis, evidence of ancient HGT, and transcriptomic comparison of the alga in symbiosis and in pure culture
doi.org/10.1111/nph.70728

Stable hypermutators revealed by the genomic landscape of genes involved in genome stability among yeast species Abstract. Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can

New work led by members of the @rokaslab.bsky.social! ☺️ 1,154 yeast genomes in the Saccharomycotina subphylum were surveyed for their relationship between reduced gene repertoires broadly associated with genome stability functions and elevated evolutionary rates.🧬
academic.oup.com/mbe/advance-...

advert text as bitmap

picture of the Schornacklab team

Plz RP. Come join us at @slcuplants.bsky.social @cam.ac.uk to study effector-targeted plant processes impacting plant cell biology and development.
www.cam.ac.uk/jobs/post-do...
www.schornacklab.net

Dual recognition of structurally unrelated mildew effectors underlies the broad-spectrum resistance of Pm3e in wheat Broad-spectrum resistance genes are highly valuable for sustainable crop protection, yet the molecular basis of their activity is often unknown. The Pm3 allelic series in wheat encodes NLR receptors t...

A wheat NLR conferring broad-spectrum resistance against powdery mildew by recognizing two structurally diverse AVR effectors. Interested? Check out our newest preprint: www.biorxiv.org/content/10.1...

Congratulations🎉🎉

Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape - Nature Plants The evolutionary diversification of an exocyst subunit was enabled by electrostatic shifts leading to its dissociation from the ancestral complex.

My main work as postdoc @plantophagy.bsky.social lab in @gmivienna.bsky.social is out in @natplants.nature.com 🌱🎉

We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.

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

A scientific figure showing speciation and explaining the concept of species delimitation, and including a quote by the paper's first author.

Check out the recent publication in Annual Reviews of Ecology, Evolution, and Systematics where the authors explore genomic species delimitation in depth. You'll see a number of #sciart figures I created to help explain some of the concepts!

www.annualreviews.org/content/jour...

Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria During pathogen attack, plants recruit beneficial microbes in a ‘cry for help’ to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonisation through vario...

📣 Now announcing the journal publication 📄 of our work in @newphyt.bsky.social on how Verticillium undermines the plant's 🌱 "cry for help": terrific work by @antonkraege.bsky.social & @wolki95.bsky.social doi.org/10.1111/nph....

In the latest issue of #G3journal, @arunsethuraman.bsky.social et al. describe biases in summary statistics, such as genetic differentiation, Tajima’s D, and estimates of theta, migration rates, and divergence for understanding genomic signatures from extinct ghost populations. buff.ly/h6bjoQc

1/2 This manifesto is the result of a collaborative effort started earlier this year at the Plant Biology Education conference in Lancaster, UK.

We are delighted to see it out and we are proud that our Comms team contributed to such an important resource for the community! 🌱

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of ge...

🚀 New preprint!
We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱
🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1
#Genomics #GeneRegulation #Maize #Soybean

Ancient origin of an urban underground mosquito Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...

How does life evolve to adapt to modern cities?

Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.

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@science.org
www.science.org/doi/10.1126/science.ady4515