Yu Sugihara
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yusugihara.bsky.social
Yu Sugihara
@yusugihara.bsky.social
290 followers 460 following 17 posts
Researcher at The Sainsbury Laboratory,
Evolution | Population genetics | Plant-microbe interactions
https://yusugihara.github.io/
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yusugihara.bsky.social
Yu Sugihara @yusugihara.bsky.social · Jul 16
🎉 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...
Reposted by Yu Sugihara
molbioevol.bsky.social
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
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
doi.org
December 1, 2025 at 9:04 AM
Reposted by Yu Sugihara
guidopuccetti.bsky.social
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
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...
journals.asm.org
December 1, 2025 at 12:00 AM
Reposted by Yu Sugihara
epigenci.bsky.social
www.biorxiv.org/content/10.1...

We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.
Genetic prediction with ARG-powered linear algebra
Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...
www.biorxiv.org
November 30, 2025 at 5:08 PM
Reposted by Yu Sugihara
apmweber.bsky.social
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...
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...
www.nature.com
November 26, 2025 at 6:00 AM
Reposted by Yu Sugihara
hassansalem.bsky.social
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 🪲🦠
Hassan, Aileen, and a local resident by the Norwich Cathedral.
November 24, 2025 at 6:42 PM
Reposted by Yu Sugihara
baym.lol
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/...
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...
www.science.org
November 20, 2025 at 9:42 PM
Reposted by Yu Sugihara
hernanaburbano.bsky.social
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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November 18, 2025 at 8:41 AM
Reposted by Yu Sugihara
smlatorreo.bsky.social
#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:
hernanaburbano.bsky.social Hernán A. Burbano @hernanaburbano.bsky.social · 13d
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

(1/n)
November 19, 2025 at 5:09 PM
Reposted by Yu Sugihara
ernstschmid.bsky.social
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
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...
biorxiv.org
November 12, 2025 at 9:26 PM
Reposted by Yu Sugihara
miguelmontez.bsky.social
📣 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...
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.
www.jic.ac.uk
November 13, 2025 at 8:34 AM
Reposted by Yu Sugihara
mpipz.bsky.social
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
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!".
November 17, 2025 at 9:00 AM
Reposted by Yu Sugihara
jlsteenwyk.bsky.social
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/...
November 13, 2025 at 8:34 PM
Reposted by Yu Sugihara
metalichen.bsky.social
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
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
November 12, 2025 at 3:46 PM
Reposted by Yu Sugihara
hittingerlab.bsky.social
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-...
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
academic.oup.com
November 11, 2025 at 4:51 PM
Reposted by Yu Sugihara
dromius.bsky.social
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
advert text as bitmap picture of the Schornacklab team
November 6, 2025 at 6:51 PM
Reposted by Yu Sugihara
lukas-kunz.bsky.social
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...
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...
www.biorxiv.org
November 2, 2025 at 1:29 PM
Reposted by Yu Sugihara
delaconcepcionjc.bsky.social
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...
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.
www.nature.com
October 31, 2025 at 1:57 PM
Reposted by Yu Sugihara
lifesciencestudios.bsky.social
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...
A scientific figure showing speciation and explaining the concept of species delimitation, and including a quote by the paper's first author.
October 29, 2025 at 1:00 PM
Reposted by Yu Sugihara
teamthomma.bsky.social
📣 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....
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...
doi.org
October 30, 2025 at 8:47 AM
Reposted by Yu Sugihara
genetics-gsa.bsky.social
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
October 29, 2025 at 6:05 PM
Reposted by Yu Sugihara
thesainsburylab.bsky.social
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! 🌱
apaterlini.bsky.social Andrea Paterlini (he/him) @apaterlini.bsky.social · Oct 29
Very excited to announce that our collaborative manifesto for 🌱 #PlantScience #Education has now been published! Educators from >10 countries and 30 institutions have contributed to it and we are incredibly proud of the final output. Here is a short thread 🧵1/4 doi.org/10.1002/ppp3...
A manifesto for plant science education
Plants provide oxygen, food, shelter, medicines and environmental services, without which human society could not exist. Tackling pressing and global challenges requires well-trained plant scientists....
doi.org
October 29, 2025 at 3:53 PM
Reposted by Yu Sugihara
kseniakrasileva.bsky.social
🚀 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
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...
biorxiv.org
October 29, 2025 at 4:47 PM
Reposted by Yu Sugihara
yukihaba.bsky.social
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.

🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
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...
www.science.org
October 25, 2025 at 4:46 AM
Reposted by Yu Sugihara
tatsuyanobori.bsky.social
@delaconcepcionjc.bsky.social from @gmivienna.bsky.social (a @johninnescentre.bsky.social alumnus) delivered his 2026 Early Career Research Award Lecture on NLR engineering and his ongoing cryo-ET work! #BiochemEvent
October 22, 2025 at 9:21 AM
Reposted by Yu Sugihara
mpmijournal.bsky.social
Just Published: "A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN," by Jana Sperschneider et al. Learn more: https://doi.org/10.1094/MPMI-04-25-0047-R
Fig. 3. AvrM3 sequence alignment and agroinfiltration assays.
October 21, 2025 at 4:47 PM