Toby Baril

EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis - BMC Genomics BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...

#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics

#TEworldwide #TEsky

www.sciencedirect.com/science/arti...

👏 Congratulations Toby for this Current Biology dispatch!
🎨 Happy to see my watercolours in it to illustrate this so-cool topic!

#illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide

I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

The influence of transposable elements on animal colouration Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transp…

Relatively specific in terms of function, but a nice review of functions in animal coloration!

www.sciencedirect.com/science/arti...

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

#TEworldwide

#TEsky #TEworldwide #Transposons #Bioinformatics #Bioconda #GenomeAnnotation #TransposableElements #Genomics #ComparativeGenomics

GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

☕Earl Grey v7.0.0 brewed fresh☕

Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix.

Happy new year to the TE folks! 🧬

github.com/TobyBaril/Ea...

Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix @nature.com @harvardmed.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...

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

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...

Excited to share our new preprint on BioRxiv!
A collaborative effort spanning many years and several labs to uncover what the germline chromosomes of Paramecium really look like. 🔗 www.biorxiv.org/content/10.1...
1/5

A comparative analysis of transposable element diversity and evolution across 75 bee genomes - BMC Genomics Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...

High‐Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon‐Driven Structural Dynamics in Fungi Evolution Long terminal repeat retrotransposons (LTR-RTs) are recognised as a significant evolutionary force capable of shaping the structure and function of the genomes in eukaryotes, including animals, plant...

High-Quality Genome Assembly of Diplocarpon coronariae Unveils LTR Retrotransposon-Driven Structural Dynamics in Fungi Evolution

doi.org/10.1111/1755...

#TEworldwide #TEsky

Awesome talk @orpsf.bsky.social! Excited to see what comes next!

#TEworldwide #TESky

#TEsky Evolution of Mutator transposons in the genomes of worms doi.org/10.1016/j.ge...

☕ Coffee break time at #EMBOMobileGenome!

Inspiring talks, lively discussions, and plenty of caffeine to keep the ideas flowing. The sun’s out, the conversations are buzzing, and tonight we’ll keep the networking going with rooftop lounge drinks 🍂🍁

Looking forward to an exciting week ahead! 🧬

At @embo.org #EMBOMobileGenome and want to connect with other TE researchers and follow the latest goings on?

Use #TEworldwide and #TEsky in your posts to be featured in the TEworldwide feed, which you can also find here:

bsky.app/profile/did:...

#TEworldwide #TEsky

Time to kick off #EMBOMobileGenome for 2025! A great selection of speakers and posters on the agenda!
#TEWorldwide #TESky

Co-opted transposons help perpetuate conserved higher-order chromosomal structures Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in ...

Transposable elements (TEs) do more than regulate genes; they help shape and preserve 3D genome structure across species.

Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.

👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!

Please feel free to share with any fungal biologists, or those interested in annotating TEs in fungal genomes, and we look forward to expanding #MycoMobilome with community contributions!

@danielcroll.bsky.social
#TEsky
#TEworldwide
#Databases
#Genomics
#Bioinformatics
#Research
#Fungi

4/ Finally, we provide guidelines for community contributions, and encourage researchers to deposit new or curated sequences, which will be incorporated into future MycoMobilome releases. This can be done through the community on Zenodo: zenodo.org/communities/...

3/ We also provide metadata to enable evaluation of TEs of interest and to determine whether further curation work is required on a case-by-case basis

2/ The initial database contains 276,641 consensus sequences after filtering to remove host genes and low-quality consensi. We provide a consistent naming convention to indicate classification confidence, including potential conflicting ORF functions

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

www.biorxiv.org/content/10.1...

#TEsky #TEworldwide

The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster Abstract. Phenotypic variation in species arises from genetic differences and environmental influences on gene expression. Differences in epigenetic modifi

"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."