JiangzhaoQian.bsky.social

ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements - Mobile DNA Background Transposable elements (TEs) are widespread mobile DNA sequences that shape genome structure, function, and evolution. Although automated tools exist for the de novo identification and class...

WOW! Very promising new tool to facilitate collaborative manual curation of TEs link.springer.com/article/10.1...

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

TEs aren’t just genomic parasites, they’re also engines of genomic novelty.

Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.

With @danielcroll.bsky.social & @guidopuccetti.bsky.social

🧬 www.nature.com/articles/s41...

#TEworldwide

What an incredible time at #EMBOMobileGenome last week! 🧬
A huge thank you to everyone who made it such a success – our speakers for their inspiring talks and thought-provoking discussions, our participants for their enthusiasm and engagement, and our team for their hard work behind the scenes 🙏🏼

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

Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi Obligate biotrophic plant pathogens like the powdery mildew fungi commit to a closely dependent relationship with their plant hosts and have lost the ability to grow and reproduce independently. Thus....

Genetic modification of obligate biotrophic pathogens like #powderymildew is often not possible, in part because they cannot be grown without a host.

We took a detour and established Arachnopeziza, closest extant relative of powdery mildew, as substitute!

onlinelibrary.wiley.com/doi/10.1111/...

TEtrimmer: a tool to automate the manual curation of transposable elements - Nature Communications Transposons are repetitive DNA sequences that are hard to identify and map accurately. TEtrimmer automates key manual steps, enabling faster and more reliable annotation of transposable elements in any genome.

Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;)

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

Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com
www.nature.com/articles/s41...

Bring your #PlantScience publishing questions for our Editors!

Catch Holly on our stand at #2025ISMPMI with @hacquardst.bsky.social, Ralph Panstruga, Ari Sadanandom, @pietrospanu.bsky.social and Ertao Wang!

📅 TODAY
⏰ 13:00–14:00
🗺 New Phytologist Foundation stand, poster hall

Transposable elements hitchhike on Starships across fungal genomes Horizontal transfer (HT) of transposable elements (TEs) is a widespread phenomenon in eukaryotes and is often associated with bursts of TE activity. This process profoundly influences genome evolution...

#Transposable elements hitchhike on Starships across #fungal genomes www.biorxiv.org/content/10.1...

I want to share our latest work on a forward simulation framework on transposable element evolution. The TE Evolution Simulation Suite, or TESS, contains three components that can simulate many scenarios of genome evolution under the impact of TEs.

🌱 We will soon open the search for a new W3 Professor in Plant Stress Resilience / Molecular Plant Physiology.

🌏Where? Germany, RWTH Aachen University @rwth.bsky.social

We plan to look widely. Please let me know, if you want to be updated on the job announcement.

#AcademicJobs

Our paper is now published in its final form: rdcu.be/elV6u @biomedcentral.bsky.social @salehlabparis.bsky.social @merklinglab.bsky.social @pasteur.fr

Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics Abstract. Starships are a recently established superfamily of giant cargo-mobilizing transposable elements in the fungal subphylum Pezizomyotina (phylum As

Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?)
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social @norwichmicro.bsky.social

scTELL: A Single-Cell ATAC-seq Tool for Locus-Specific Transposable Element Identification in Chromatin Accessibility

#TEsky #TEworldwide

www.researchsquare.com/article/rs-6...

Harnessing transposable elements for plant functional genomics and genome engineering Transposable elements (TEs) constitute a large portion of many plant genomes and play important roles in regulating gene expression and in driving genome evolution and crop domestication. Despite advances in understanding the functions and mechanisms of TEs, a comprehensive review of their integrated knowledge and cutting-edge biotechnological applications of TEs is still needed. We provide a thorough overview that connects discoveries, mechanisms, and technologies associated with plant TEs. We discuss the identification and function of TEs driven by functional genomics, epigenetic regulation of TEs, and utilization of active TEs in plant functional genomics and genome engineering. In summary, expanding the knowledge and application of TEs will be beneficial to crop breeding and plant synthetic biology in the future.

Harnessing transposable elements for plant functional genomics and genome engineering #plantscience

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

It's been a while because I've felt distracted lately with...*gestures at everything* but, I've gone and updated TE Hub @tehub.bsky.social with new tools, databases and TE lineages tehub.org #TEsky

📣 #EMBOMobileGenome is open for registrations!

Assembling experts in genomics, epigenetics, structural biology, evolutionary biology, and developmental biology to discuss the broad impact of TEs on organismal biology. 🧬🔍

📜 Submit abstract by 29 July!
👉🏼 https://s.embl.org/mge25-01-bl

Yes, that will be great if this tutorial can be placed there

TEtrimmerGUI designed to improve your TE consensus library YouTube video by Zhao Jiang

We created a comprehensive video tutorial on how to use TEtrimmerGUI to curate your TE consensus sequences.
Watch it here:
youtu.be/52GYZUQyzSE?...

Great tall from @clementgoubert.bsky.social to present GraffiTE: a pipline that finds polymorphic TE in genomes
#PAG32
github.com/cgroza/Graff...

Fungal phylogeny highlighting genome size changes

Summary of genome size variation among groups

@tbadet.bsky.social and I have a preprint out on transposon silencing in fungi!

Genome size evolution is fascinating and showcases the dynamic nature of transposon activation.

What we understand less are the dynamics of transposon defense systems encoded by the genomes.

doi.org/10.1101/2025...

GenomeDelta: detecting recent transposable element invasions without repeat library - Genome Biology We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-qualit...

Our novel tool for finding recent TE invasions without repeat library - great work by amazing student Riccardo (not yet on bsky) genomebiology.biomedcentral.com/articles/10....

Now hiring:

Are you a technician? Do you enjoy the lab? Plants 🌱? DNA 🧬? Microscopes 🔬?

We are looking for you! We are looking for a Biological Technical Assistant for the new molecular botany lab at @rwth.bsky.social Aachen. Please apply!

www.biologie.rwth-aachen.de/cms/biologie...