Björn Usadel

Cell wall patterning regulates plant stem cell dynamics The plant cell wall regulates development through spatiotemporal modulation of its chemical and mechanical properties. Pectin methylesterification is recognized as a rheological switch controlling wal...

Out in @science.org this week:
PME5 is sequestered in the nucleus and released during cytokinesis allowing its activity to be timed with cell division.

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

#PlantScience
#PlantSci

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...

Helixer: a tool for ab initio gene annotation with broad taxonomic coverage. @usadellab.bsky.social @apmweber.bsky.social @weberlab.bsky.social

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

Fig. 1.Current stage of tomato and wild relative genome sequencing.

🧬🍅 SPECIAL ISSUE REVIEW 🍅🧬

Recent breakthroughs in genome sequencing have transformed tomato research, unlocking key wild germplasm traits 🌍
Rose et al. outline how these well-characterized genetic resources can be used to improve tomato research 🔬

🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪

We are looking for a Head of Cell Biology here at @kwsgroup.bsky.social Vegetables.

This is a permanent, full-time position located in Wageningen, Netherlands.

jobs.kws.com/job/Wagening...

#PlantScience #PlantSciJobs #PlantScienceJobs #PlantCellBiology #PlantBreeding #PlantSciJob #PlantScienceJob

Ripe tomato fruit on its truss (credit: Marine Honoré).

📝 SPECIAL ISSUE EDITORIAL 📝

🍅 Tomato 🍅

🔎 Guest editors Gibon, Beckles, Osorio & Ezura dive into the reviews, technical innovations and original research articles in this special issue that address the major challenges facing the tomato industry 🍅

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪

W1-Juniorprofessur für Plastidäre Homöostase (m/w/d) - Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU) Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU) bietet Stelle als W1-Juniorprofessur für Plastidäre Homöostase (m/w/d) in Kaiserslautern - jetzt bewerben!

Junior Professorship Plastid Homeostasis. Kaiserslautern, Germany.
#plantscijobs #plantscijob
www.academics.de/jobs/w1-juni...

W2-Professur für Pflanzenphysiologie (m/w/d) - Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU) Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU) bietet Stelle als W2-Professur für Pflanzenphysiologie (m/w/d) in Kaiserslautern - jetzt bewerben!

Professorship Plant Physiology. Kaiserslautern, Germany
#plantscijobs #plantscijob
www.academics.de/jobs/w2-prof...

Thanks this really points to undersampling. Luckily things get better overtime with potential training data.

Thanks. The weevils is interesting. Did you try it on Chrysomeloida by any chance? and/or is this across weevil families?

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...

Performance approaches data-supported references across plants, fungi, vertebrates, and invertebrates.

Inference is fast: human genome in <9 h on a single GPU.

@alisandra-denton.bsky.social
@usadellab.bsky.social
@sebtriesch.bsky.social
@weberlab.bsky.social

CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...

And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...

Perspective here:
www.science.org/doi/10.1126/...

Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding - Nature Communications Eggplants are important vegetables worldwide. Here, the authors report 40 genome assemblies of Solanum melongena, its progenitor S. insanum and the allied species S. incanum to construct two pangenome...

Tomorrow Luciana Gaccione from Lorenzo Barchi's lab will explain on our @nanoporetech.com day at HHU Düsseldorf, how to turn what we sequenced with 9.41 technology (!) into a high quality pangenome. If you can't make it, read all about it here as well: www.nature.com/articles/s41...

8/8
And iii) chlorogenic acid metabolism potentially caused by a GDSL-lipase like gene
www.nature.com/articles/s41...

7/8
ii) fusarium wilt resistance with QTL comprising RPP13-like disease resistance genes as well as a AT-hook motif nuclear-localized (AHL) protein
www.nature.com/articles/s41...

6/8
We also analyzed 218 traits (agronomic, resistance to biotic and abiotic stresses, fruit metabolic composition) scored in 3 field trials, in Spain, Italy and Türkiye among them i) prickliness.
www.nature.com/articles/s41...
where we could pinpoint an interesting LOG translocation.

5/8
The “core” genome of eggplant was found to consist of around 16,300 gene families, (present in all varieties) while around 4,000 gene families were “dispensable” (i.e. they were present in only one or few varieties).

4/8
We then focused on 368 varieties, representative of the worldwide phenotypic and genetic diversity of eggplant and comprising its wild progenitors, Solanum incanum and Solanum insanum. We constructed a graphical pangenome…
www.nature.com/articles/s41...

3/8
This led to the observation that for instance, the varieties coming from India and South-East Asia have retained the non-purple skin colour and the spiny leaves characteristic of their wild ancestors, while these traits were progressively lost in the other geographical areas.

2/8
We had started from a large worldwide collection of 3,400 eggplant varieties and wild progenitors and used it to reconstruct its domestication history in India and South-East Asia, and its later expansion doi.org/10.1111/tpj..... www.nature.com/articles/s41...

Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding - Nature Communications Eggplants are important vegetables worldwide. Here, the authors report 40 genome assemblies of Solanum melongena, its progenitor S. insanum and the allied species S. incanum to construct two pangenome...

1/8
How do graph pangenomes and panphenomes help breeding eggplant? doi.org/10.1038/s414.... This feat would not have been possible without a large team of 24 researchers from 7 countries.

#PlantSciJobs!!

Systems-level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation Plant molecular adaptation to plant growth promoting bacteria (PGPB) under nutrient stress remains unclear, yet is essential for advancing PGPB use in agriculture. The model grass Brachypodium dystach...

In our new pre-print 📝we dissect how #plants🌾 adapt their metabolism under #Nitrogen limitation when #beneficial #Pseudomonas 🦠are present. You can compare #Noninvasive #Phenotype 📸 during 3 weeks with #lipidomc and #proteomic results at specific 🕰️.

www.biorxiv.org/content/10.1...
🧪 #PlantSci #PMI

Postdoctoral Research Position in Plant–Microbe Interactions | University of Cologne, Germany The Saur Lab at the University of Cologne invites applications for a postdoctoral position in molecular plant–microbe interactions. This ERC-funded role offers an opportunity to study non-host resistance to fungal pathogens in cereal crops within one of Europe’s top research environments.

Postdoctoral Research Position in Plant–Microbe Interactions | University of Cologne, Germany

The Saur Lab at the University of Cologne invites applications for a postdoctoral position in molecular plant–microbe interactions. This ERC-funded role offers an opportunity to study non-host resistance…

Job posting. We look for a Full Professor (W3) of Stress Resilience of Plants at the RWTH Aachen.

We are looking for a colleague to join us at RWTH Aachen University:

🌱 Full Professor in Stress Resilience of Plants (W3 tenured)

📌What are we looking for? Someone working with us strategically at the interface of plant biology/ physiology/ resilience

#academicjobs #facultyjobs #PlantJobs

1/4

Hi all @plantsciencedbg.bsky.social members and other 🌽community folks, #MBP2026 🌱 is no open for registration. Please 🏄‍♀️ to: www.pflanzen-molekularbiologie.de/en/conferenc...

Assistant Professor in Austin, TX for The University of Texas at Austin Exciting opportunity in Austin, TX for The University of Texas at Austin as a Assistant Professor

Tenure-Track Plant Biology Assistant Professor position at UT Austin MBS. Review of the applications starts Nov. 1! Please spread the words🤠🌱🌼🌽🫛🍃🌾
jobs.plantae.org/jobs/2176440...

🎉We have announced a new professorship at the University of Gothenburg 🇸🇪 to celebrate our Crown Princess’s 50th birthday!
🌿Broad focus on biodiversity — from microbes to modelling
📢A fantastic opportunity for researchers working across scales and disciplines!

🔗 web103.reachmee.com/ext/I005/103...

Now we just need more target journal support (esp. plant journals) but this is really something needed....

Very nice that sounds really cool! Congrats