David T

Im so happy to share this part of my PhD thesis just right now in ⁦@NatureComms⁩. Check it out! Implications of the 3D chromatin organization for genome evolution in a fungal plant pathogen Special thanks to ⁦@MFSeidl⁩ and ⁦@Team_Thomma⁩ nature.com/articles/s4146…

Nature research paper: Ancient co-option of LTR retrotransposons as yeast centromeres go.nature.com/404vd9X

Vorholt Lab re-created endosymbiosis in the lab: injected bacteria into a fungus and evolved a heritable partnership. Evolution, fast-forwarded. doi.org/10.1038/s41586…

Check out our recent preprint on the structure of a non C-JID TNL resistosome from flax. We are very proud of the persistence of Natsumi who got this long running project over the line and a congratulations to all involved. Check it out... doi.org/10.64898/2026.…

Genome contamination may lead to an overestimation of horizontal gene transfer inferences | Nature Communications nature.com/articles/s4146…

📢 Three new #bioRxiv preprints from our team on holocentric chromosomes. Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇

Big congrats to PhD @Ken_M_Mugambi for pulling together this amazing piece of work 🫡 This study details the genome biology of the largest #AMF genome (G. margarita) and its intricate links with its🦠 endosymbiont and 🌱hosts 😀 biorxiv.org/content/10.648…

Join us in Norwich this July for the TSL Summer Conference in Plant-Microbe Interactions! ☀️🌱🧬 Discuss the latest approaches & discoveries in plant health with international keynote and local speakers. APPLY by 30 March '26 ⬇️ Click link for more info tsl.ac.uk/tsl-summer-con…

New online! Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription dlvr.it/TQKgsH

Can we design mutations that predictably bias proteins towards desired conformational states? Today in @ScienceMagazine, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations. science.org/doi/10.1126/sc…

Epigenetics Update - Stress controls heterochromatin inheritance via histone H3 ubiquitylation go.nature.com/4pwTxvp Shiv I. S. Grewal reporting in Nature #Epigenetics #Heterochromatin #Ubiquitylation --- Gain deeper insights into gene regulation; epigenometech.com

Salicylic acid contributes to plant defense against a necrotroph: evidence from a transgenic NahG-expressing strain in Botrytis cinerea. biorxiv.org/content/10.648… #biorxiv_plants

How does AlphaFold select protein conformations? Its transformer model (Evoformer) associates them with sparse sequence patterns. We developed a method to identify these patterns readily🧵 biorxiv.org/content/10.648…

New online! A genomic and epigenomic view of human centromeres bit.ly/4jvn3A8

Evolutionary transcriptomics unveils rapid changes of gene expression patterns in flowering plants cell.com/cell/fulltext/…

The one that abstained: Psilocybe fuscofulva genome suggests two recent origins of the psilocybin gene cluster in Psilocybe biorxiv.org/content/10.648… #biorxiv_evobio

Well done, Akie! Identification of a peptide hormone-receptor module bypassing the ABA signaling to close stomata upon drought. A big breakthrough🍃😊 -Local peptide signalling induces stomatal closure under drought stress @NatureComms nature.com/articles/s4146…

Abstract submission and registration for the #47NPS Extreme Heat: extending the thermal limits of life, are open! 2–5 June 2026 Travel grant, selected speaker application deadline: 2 February 2026 Poster abstract deadline: 2 March 2026 Full details at newphytologist.org/events/47-nps

What sets the mutation rate of a cell type in an animal species? biorxiv.org/content/10.648… 🧬🖥️🧪

Many people think of the genome as a string of "letters." The human genome, say, has 3.2 billion base pairs of DNA organized across 23 pairs of chromosomes. But the genome is a 3D object. Genes located on entirely different chromosomes might be clustered together. Mutations in these "distant" genes can lead to disease in surprising ways. For a new paper in @Nature, researchers released several "maps" of human genomes from two types of cells: embryonic stem cells and fibroblasts. They compared methods to see which ones are least biased, and found many long-range interactions between genes. The article does a good job explaining how “the genome is organized at different scales”: > On a single chromosome, histones control which parts of the DNA sequence are accessible and expressed. > At the scale of hundreds of thousands of bases, “chromatin loops in a dynamic manner,” the authors write, bringing distant genes closer together. > Across chromosomes, sequences "cluster together in space to form subnuclear compartments." Examples abound. Enhancers, for example, are short DNA sequences that regulate the expression of far away genes. They do this by *physically* touching the genes they control; a protein called cohesin grabs the DNA and tugs it into big loops. Even promoters, which are thought of as being associated with one gene or operon, can cluster together across many genes! A protein, Ronin, grabs promoters and pulls them together. This is apparently done mostly for genes that tend to be "on," as it helps enzymes find genes faster/not have to diffuse far away to find targets. (This also happens with genes that tend to be "off;" so-called polycomb proteins grab onto promoters, cluster them up, and silence all of them at once. It's a way for the cell to conserve energy.) One consequence of this spooky "action-at-a-distance" is that diseases might arise from mutations in unexpected locations. Editing these regulatory sequences, in other words, might in turn affect a gene located on an entirely different chromosome that *is* associated with that disease. Genetic mutations linked to autism, for example, are known to disrupt the 3D organization of the genome. A single deletion at a gene, TAL1, also affects its ability to form long-range chromatin interactions with other genes, leading to leukemia. There are probably many other, as-yet-undiscovered, instances of this.

Evolution of HMA-integrated tandem kinases accompanied by expansion of target pathogens biorxiv.org/content/10.648… #biorxiv_plants