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Clément Goubert @clementgoubert.bsky.social · 23d

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation

Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

www.cell.com

Clément Goubert @clementgoubert.bsky.social · Aug 28

Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence journals.plos.org/plosgenetics...

Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence

Author summary Transposable elements (TEs) are short, self-replicating DNA sequences found in nearly all genomes. While they can be harmful to their hosts, many organisms have evolved defence systems,...

journals.plos.org

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Clément Goubert @clementgoubert.bsky.social · Aug 26

A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes -- by the excellent @valentinapeona.bsky.social link.springer.com/protocol/10....

A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes

Transposable elements (TEs) can play a huge role in shaping the structure and evolution of genes and genomes, but it can be difficult, especially in non-model organisms, to confidently characterize th...

link.springer.com

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Clément Goubert @clementgoubert.bsky.social · Jul 25

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties

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

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties

Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fi...

www.biorxiv.org

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Clément Goubert @clementgoubert.bsky.social · Jul 23

How the complex issue of delineating #Transposons families plays out in the interpretation of epigenetic experiments. Congrats Xun Chen and @guilbourque.bsky.social for leading this work, and thank you for having me on this! www.science.org/doi/10.1126/... #TEsky

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage

A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

www.science.org

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Clément Goubert @clementgoubert.bsky.social · Jun 2

Challenging the TE burst hypothesis in the adaptive radiation of Galápagos Asteraceae trees (Scalesia) with @naturalselection.bsky.social and team!
mobilednajournal.biomedcentral.com/articles/10....

No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts - Mobile DNA

Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between specie...

mobilednajournal.biomedcentral.com

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Clément Goubert @clementgoubert.bsky.social · May 27

Waho this is impressive: github.com/zeqianli/tgv

GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

github.com

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Reposted by Clément Goubert

Magdalena Skipper @magdalenaskipper.bsky.social · Apr 24

New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles

159 years after Mendel published his work, this is a real delight (especially for a geneticist)

🧪
@nature.com

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

Genomic and genetic insights into Mendel’s pea genes - Nature

Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...

www.nature.com

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Clément Goubert @clementgoubert.bsky.social · Apr 29

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin www.biorxiv.org/content/10.1...

www.biorxiv.org

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Reposted by Clément Goubert

Travis Wheeler @wheelerlab.org · Apr 22

🧬🖥️
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)

(crates.io/crates/nail, github.com/TravisWheele...)

Thanks Evangelos!

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Clément Goubert @clementgoubert.bsky.social · Apr 25

go.nature.com/3S27sLp

Celebrating DNA Day with transposable elements

Each year on DNA Day, we celebrate the DNA double helix structure and the Human Genome Project's completion. Here we dive into a fascinating genomic component: transposable elements. Once seen as mere...

go.nature.com

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Reposted by Clément Goubert

Dr. Stephanie @punkrockscience.bsky.social · Mar 24

The writing’s been on the wall for a while, and in case anyone was unaware: YOUR GENOMIC DATA IS THE MOST VALUABLE ASSET THEY HAVE LEFT.

Delete your data. Make sure you opt-out of any opt-outable options.

Tell your friends and family - you know that technophobe cousin missed the memo. 🧪

Column | Delete your DNA from 23andMe right now

The genetic information company declared bankruptcy on Sunday, and California’s attorney general has issued a privacy “consumer alert.”

www.washingtonpost.com

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Clément Goubert @clementgoubert.bsky.social · Mar 24

Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰) www.pnas.org/doi/full/10.... #TEsky

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Clément Goubert @clementgoubert.bsky.social · Mar 19

Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence www.biorxiv.org/content/10.1...

Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence

Transposable element (TE) invasions pose risks to both the TE and the host. All copies of a TE may be lost via genetic drift, or host populations may suffer fitness declines, potentially leading to ex...

www.biorxiv.org

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Clément Goubert @clementgoubert.bsky.social · Mar 12

#Transposons are just the best!

Unnati Sonawala @uprogress.bsky.social · Mar 11

Cool study! Plant defense usually means looking 'not-diseased,' making these genes invisible until lost. But here, the authors found that a 254bp transposon in bHLH35 boosts anthocyanins, visually camouflaging the plant from herbivores. A defense you can see!

Nature Ecology & Evolution @natecoevo.nature.com · Mar 11

Multi-omics analysis reveals that a 254-bp transposon induces defensive camouflage in an alpine plant and reduces herbivory by caterpillars of a specialist butterfly. Protective effects of this camouflage are reflected in the long-term dynamics of co-evolving plant and butterfly populations.

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Reposted by Clément Goubert

Adrià Auladell @adriaula.bsky.social · Mar 12

Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species.

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Clément Goubert @clementgoubert.bsky.social · Mar 10

Worth mentioning that hmm models for D. melanogaster elements in DFAM are now seeded from additional genomes (beyond the dm6 reference), including 13 genomes from Rech. et al., 2022 (www.nature.com/articles/s41...)

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Clément Goubert @clementgoubert.bsky.social · Mar 10

P element entry: dfam.org/family/DF003...

Dfam

Open database of transposable elements and repetitive DNA families

dfam.org

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Clément Goubert @clementgoubert.bsky.social · Mar 10

Following new user submissions many previously DFAM fly model of TE families were revisited/updated, absent elements (such as P) were added, and when applicable, aliases between DFAM/Repbase/Flybase/BGDP and other publications are reported!

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Clément Goubert @clementgoubert.bsky.social · Mar 10

DFAM (database of transposable elements) 3.9 is out! A lot of cool new stuff and a special update for Drosophila melanogaster... 1/2 #Transposon #DFAM

Dfam Database of Transposable Elements @dfam.bsky.social · Mar 10

Today we released Dfam 3.9 with many new community submissions and the result of a thorough curation and update of the Drosophila Melanogaster library. www.dfam.org (release notes: www.dfam.org/releases/Dfa...)

Dfam

Open database of transposable elements and repetitive DNA families

www.dfam.org

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Clément Goubert @clementgoubert.bsky.social · Mar 7

Cool stuff from the Trono lab, as usual! Zinc-finger proteins with a co-opted capsid domain
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...

www.biorxiv.org

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Reposted by Clément Goubert

plantgenomics.bsky.social @plantgenomics.bsky.social · Mar 3

LOCATE: using Long-read to Characterize All Transposable Elements
doi.org/10.1101/2025...

Mapping-based Genome Size Estimation
doi.org/10.1101/607390

#Genomics #Bioinformatics #OpenScience

LOCATE: using Long-read to Characterize All Transposable Elements

Transposons constitute ~45% of the human genome, driving gene evolution and contributing to disease, but their repetitive nature complicates the identification of new insertions. We present LOCATE (Lo...

doi.org

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Reposted by Clément Goubert

Francois Sabot @francoissabot.bsky.social · Mar 3

Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪

In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5

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

www.biorxiv.org

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Clément Goubert @clementgoubert.bsky.social · Feb 24

RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate
www.nature.com/articles/s41...

Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells - Nature Genetics

The N6-methyladenosine reader YTHDC2 recruits TET1 to remove 5-methylcytosine from LTR7/HERV-H loci in human embryonic stem cells. The YTHDC2/LTR7 pathway inhibits neural fate commitment.

www.nature.com

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Clément Goubert @clementgoubert.bsky.social · Feb 18

Very promising approach to characterize the mobilome in pangenomes from ! I wonder how this compares/complements to Pantera (@piosierra.bsky.social) and GraffiTE www.biorxiv.org/content/10.1... #TESky #SV #Pangenomes

Pannagram: unbiased pangenome alignment and the Mobilome calling

Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple geno...

www.biorxiv.org

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