Excited to share “Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens” dx.doi.org/10.1111/tpj.... @frankelab.bsky.social @nancy-choudhary.bsky.social @shakunthalan.bsky.social @puckerlab.bsky.social #Genomics #SpecializedMetabolism

Congratulations to Nick Irwin, group leader at the GMI of the @oeaw.bsky.social, who was awarded a Starting Grant from the @erc.europa.eu! He and his group will investigate the origins of phytohormone pathways in land plants. More: www.oeaw.ac.at/gmi/detail/n...

Just finished reading "Microbe Hunters" (1926). What a book! It brings to life the great discoveries of microbiology - and, even more, the people behind them: Leeuwenhoek, Pasteur, Koch, and others who revealed the invisible world shaping disease, wine, beer, and food 1/5

In our newest issue, we interview Jiayang Li, who studies plant molecular genetics and crop breeding, particularly in rice, at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. Find out more here: www.cell.com/current-biol...

Jiayang Li

Interview with Jiayang Li, who studies plant molecular genetics and crop breeding, particularly in rice, at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences.

cell.com

Okay this one’s gonna be controversial. In our new preprint, we show that the canonical #Klebsiella pneumoniae 🦠 virulence factors and strain lineage are decoupled from infection severity and patient outcomes. This was a surprise to us #IDSky #KlebClub #MicroSky 🧪 www.medrxiv.org/content/10.6...

Agrobacterium-mediated transient expression has revolutionized plant research, but is largely confined to solanaceous species. This study shows that an engineered strain allows efficient transient expression across diverse dicot crop species. 🧪 #AcademicSky #plants plos.io/3W0hqlP

Haven't used this is in a while, but a new paper from the group is a good excuse. This is monster of a paper from Sebastian Kaiser about the evolution of non-ribosomal peptides. www.nature.com/articles/s41...

Drift, selection and recombination bias drive the evolution of a non-ribosomal peptide - Nature Ecology & Evolution

The structural diversity of non-ribosomal peptides is largely determined by recombination. This study shows that selection, genetic drift and biased recombination rates contribute to the diversity of ...

nature.com

The title really intrigued me, but I couldn't have imagined how much I would love this paper! Actually, I was so excited by the findings that I wrote a @prelights.bsky.social😄 If you haven't read it yet, go dive into this amazing paper lead by @noelponte.bsky.social 🤩 www.biorxiv.org/content/10.6...

Brassinosteroid receptors reveal conserved features of exon-embedded gene regulation

Precise quantitative and spatial control of plant gene expression is typically attributed to cis-regulatory elements in promoters and other non-coding sequences. The extent to which exon-encoded regul...

biorxiv.org

preLights@prelights.bsky.social · last wk.

Hide and seek: exonic sequences harbor cis regulatory elements and regulate spatial expression of brassinosteroids receptors. #PlantBiology @karimaelm.bsky.social covers a recent #preprint by Raúl Denia-Mondéjar et al. @noelponte.bsky.social #preLight ⬇️ prelights.biologists.com/highlights/b...

Excited to share this work from our group, together with the Jackson and Beisel labs! 🧬 We found that aminoacylated tRNA fragments can act as signals to activate bacterial immunity, boosting protection by Cas12a3. Very cool biology, and a great collaboration! www.biorxiv.org/content/10.6...

Aminoacylated tRNA tails trigger auxiliary bacterial immunity

Bacterial immune systems cleave, modify or sequester transfer RNAs (tRNAs) to block viral replication and dissemination. While considered an endpoint of immune activation in bacteria, cleaved tRNA fra...

biorxiv.org

Sorek Lab@soreklab.bsky.social · last wk.

Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity

How we are approaching AI at openRxiv - new blog post prompted by growing adoption by researchers, submission patterns, and questions from the community openrxiv.org/approach-to-... 1/n

What happens when applicants review each other's grants? Our two-year trial with @volkswagenstiftung.de reveals high applicant backing, faster reviews, and surprisingly different funding choices than traditional panels: doi.org/10.6084/m9.f...

Dear @dfg.de in light of these rates, I really think it’s worth starting a scheme like @fwf-at.bsky.social www.fwf.ac.at/en/funding/p... many grants that are positively evaluated by ~10 reviewers won’t get funded 😔

News: millions of years ago, hybridization gave rise to a tetraploid #fish with two distinct parental subgenomes & this is fascinating: as young barbels develop, they switch from using opsins from one subgenome as larvae to those from the other as adults, fine-tuning their colour #vision! 👁️🌈.

I've complained on here a few times about synteny plots that are harder to read than they need to be. I decided it was time to actaully do something about it: introducing SynTangle, a tool for untangling whole-genome synteny plots github.com/Hanliconius/... 1/

GitHub - Hanliconius/SynTangle: On synteny plots, intrinsic tangledness is real, layout tangledness is noise. This tool is for removing layout tangledness.

On synteny plots, intrinsic tangledness is real, layout tangledness is noise. This tool is for removing layout tangledness. - Hanliconius/SynTangle

github.com

Joe Hanly@hanliconius.bsky.social · last mo.

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

This is a truly startling paper. It shows that mRNA can perform regulatory functions *in addition to* its role in encoding a protein. In other words, the distinction between protein-coding RNA and noncoding regulatory RNA is fuzzy. /1 www.science.org/doi/10.1126/...

Regulation of target gene expression by chromatin-associated protein-coding transcripts in plants

Protein-coding transcripts are regarded as intermediates that mediate DNA-to-protein information flow, leaving their noncoding regulatory potential largely underappreciated. Genome-wide profiling of R...

science.org

Excited to share this bioRxiv where we identify another host target for a Magnaporthe effector. Here we characterise the interaction between the zinc finger fold effector (Tie1) to a conserved family of transcription factors called the Tubby-like F-box proteins (TLPs) www.biorxiv.org/content/10.6...

A Blast Fungus Effector Targets a Tubby-like F-box Protein to Suppress Plant Immunity

The blast fungus Magnaporthe oryzae is one of the most destructive pathogens of rice, secreting effector proteins that reprogram host cells to enable infection. Identifying plant targets of these fung...

biorxiv.org

New preprint 📄 Should long-read RNA-seq counts be normalized? We benchmarked 5 normalization methods × 5 quantifiers on PacBio and ONT, using spike-ins and matched Illumina as ground truth 🧵 www.biorxiv.org/content/10.6...

Systematic evaluation of transcript normalization methods and quantification pipelines across long-read sequencing platforms

Long-read RNA sequencing (lrRNA-seq) has transformed transcriptomics by enabling full-length isoform resolution, yet transcript quantification remains confounded by platform-dependent length biases an...

biorxiv.org

🌱 How do plants read chitin length? The receptor CHIP13 works like a molecular measuring tape. What began 13 years ago with a recalcitrant protein is now in @science.org. Thanks to all my co-authors and colleagues! doi.org/10.1126/scie...

Structural basis for size-selective perception of chitin in plants | Science www.science.org/doi/10.1126/...

Structural basis for size-selective perception of chitin in plants

Plants detect microbes through pattern recognition receptors that perceive conserved microbial surface motifs known as microbe-associated molecular patterns (MAMPs). Lysin motif (LysM) receptors recog...

science.org

A new preprint by @amirfromm.bsky.social 📣 How do protists fight viruses in nature? Using single-cell sequencing in an isolated alpine lake, we uncover natural giant-virus infections and reveal the induction of viperin, an ancient antiviral defense, in wild protists 🏔️🦠->

Single-cell-resolved natural giant virus infections reveal conserved protist immunity

Single-cell eukaryotes (protists) are key players in microbial ecosystems. Yet, our understanding of how they interact with viruses in nature and how antiviral defenses shape these relationships remai...

biorxiv.org

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Our friend the @shlezingerlab.bsky.social is hiring! Highly recommended. Working on the fascinating unknown world of mycoviruses. Her 1st postdoc, Marina Campos Rocha, just started her independent academic position.

New version of our paper on gene tree topologies under duplication, loss, and coalescence. (Led by @smishra677.bsky.social) 1st version was wrong: we should have been conditioning all our expected branch lengths on seeing a duplication at all. Now fixed! www.biorxiv.org/content/10.6...

Distribution of Gene Tree Topologies with Duplication, Loss, and Coalescence

Motivation: Many methods can be used to infer the number and timing of gene duplication and loss events from gene trees. Most such reconciliation methods use a model of gene duplication that does not ...

biorxiv.org

Anyone brave enough for an adventure in the uncharted waters of plant immunity and cell biology? We have a PhD studentship available as part of the NRP DTP - join us! biodtp.norwichresearchpark.ac.uk/projects/how...

How do the connections between a cell and its neighbours control how a cell responds? (FAULKNER_J27DTP) | Doctoral Training Partnership

Plant cells are connected to their neighbours via ‘tubes’ called plasmodesmata, creating an interconnected cytoplasm that joins cells within and between tissues and organs.

biodtp.norwichresearchpark.ac.uk

Kingdom-wide comparative transcriptomics reveals deeply conserved and predictable stress response programs across Viridiplantae #research #MolecularPlant cell.com/molecular-pl...

Beetles secrete jelly to embed & sustain symbionts with impossibly tiny genomes🪲 But what is this jelly made of? And how does it help maintain a partnership that has lasted over 62 million years? Thrilled to share our latest, out now in @natcomms.nature.com! www.nature.com/articles/s41...

Yellow protein co-opted to sustain obligate symbiosis in leaf beetles - Nature Communications

Insects have evolved diverse strategies to protect their genome-reduced symbionts during vertical transmission. Here, authors show that tortoise beetles have co-opted a Yellow protein to form spheres ...

nature.com

John Innes Centre@johninnescentre.bsky.social · 3w ago

NEWS - Beetles build with a yellow pigment gene 🪲 More than 80 years ago, scientists discovered that differences in yellow pigmentation were critical to courtship success and failure for fruit flies. 🧵

Two PhD opportunities in our lab: 1. What do bacterial NLR proteins do beyond phage defence? Join us to explore how these proteins regulate viability, multicellular development and antibiotic production in Streptomyces. Apply 👉 shorturl.at/N8Abx #PhD #Microsky #Bioinformatics #Streptomyces

From Defence to Antibiotic production: Uncovering New Roles for NLR Signalling in Multicellular Bacteria (SCHLIMPERT_J27DTP) | Doctoral Training Partnership

Nucleotide-binding and oligomerisation domain-like receptors (NLRs) are famous for driving immune responses in plants and animals. However, their extensive presence in multicellular…

shorturl.at

This past summer, work from my dissertation was published in MBE ! We found that the sex ratio supergene in Formica likely has two origins, one Nearctic and one Palearctic. This likely happened due to recombination between two standing haplotypes that underlie colony queen number! 🐜🐜

Molecular Biology and Evolution@molbioevol.bsky.social · 4mo ago

@g-lagunasrobles.bsky.social et al. used WGS in Formica ants to study supergene diversification and gain of function, finding evidence for two origins of the MD haplotype. 🔗 doi.org/10.1093/molbev/msag135 #evobio #molbio #supergene

Two years ago, I asked @rorycraig.bsky.social sky.social during his visit to Virginia Tech about the viral TET gene, sparking an awesome collaboration with @alexdemendoza.bsky.social! What a way to wrap up my PhD in the Aylward Lab! Such an elusive virus, yet a little giant genetic engineer itself.

Alex de Mendoza@alexdemendoza.bsky.social · 2w ago

How can a #GiantVirus 👾 lurk inside the host genome undetected? We find that epigenetic conflict lies at the centre of the ⚖️ between infection and co-existence with the host. Great collaboration with the Aylward lab out in @biorxivpreprint.bsky.social: www.biorxiv.org/content/10.6...

🔬Postdoc position available! Interested in uncovering the molecular mechanisms underlying host-endosymbiont interactions? Join our group and help us explore these fascinating biological partnerships! Deadline: 29. Oct Details & application: karriere.hhu.de/index.php?ac... Please spread the word!

Postdoc (m/f/d) in Endosymbiosis Research

karriere.hhu.de