Clément Goubert

Clément Goubert

@clementgoubert.bsky.social

🤘🧬 Transposable ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ Elements 🧬🤘 ---- Assistant Research Professor @wheelerlab.org University of Arizona

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Clément Goubert
@clementgoubert.bsky.social

The new GraffiTE v1.1 is out 🎉 github.com/cgroza/Graff... Find, annotate and genotype polymorphic TE insertions, now with epigenetic mapping, thanks to @cgroza.bsky.social's magic 🪄 Enjoy!

github.comGitHub - cgroza/GraffiTE: GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using geno...GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs. - cgroza/Gra...
Clément Goubert
@clementgoubert.bsky.social

Major development in the #Transposon world! Repbase is joining the Dfam project and becomes open-access! link.springer.com/article/10.1...

link.springer.comUnifying Repbase and Dfam: a new open foundation for transposable element research - Mobile DNARepbase and Dfam, the two foundational resources for transposable element annotation, are being unified into a single, fully open access framework, with Repbase released under CC-0 and its core curati...
Dfam Database of Transposable Elements@dfam.bsky.social

A New Open Foundation for TE Research: GIRI is transitioning the full Repbase collection to an open-access license and joining the Dfam effort to help build a unified open resource for transposable element research. Full announcement: tinyurl.com/48665xss

Clément Goubert
@clementgoubert.bsky.social

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

journals.plos.orgRapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defenceAuthor 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,...
Clément Goubert
@clementgoubert.bsky.social

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....

link.springer.comA Concise Guide for the Characterization and Curation of Transposable Elements in Insect GenomesTransposable 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...
Clément Goubert
@clementgoubert.bsky.social

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties www.biorxiv.org/content/10.1...

biorxiv.orgAdaptive P-element insertions in a long non-coding RNA are associated with unique silencing propertiesTransposable 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...
Clément Goubert
@clementgoubert.bsky.social

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

science.orgA phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineageA phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.
Clément Goubert
@clementgoubert.bsky.social

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....

mobilednajournal.biomedcentral.comNo evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts - Mobile DNATransposable 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...

Clément Goubert reposted

Magdalena Skipper
@magdalenaskipper.bsky.social

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...

nature.comGenomic and genetic insights into Mendel’s pea genes - NatureCharacterization 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...
Clément Goubert
@clementgoubert.bsky.social

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...

biorxiv.orgRapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defenceTransposable 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...
Clément Goubert
@clementgoubert.bsky.social

#Transposons are just the best!

Unnati Sonawala@uprogress.bsky.social

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!

Clément Goubert reposted

Adrià Auladell
@adriaula.bsky.social

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

bioRxivpreprint@biorxivpreprint.bsky.social

A natural mechanism of eukaryotic horizontal gene transfer https://www.biorxiv.org/content/10.1101/2025.02.28.640899v1

Clément Goubert
@clementgoubert.bsky.social

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

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.orgDfamOpen database of transposable elements and repetitive DNA families
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Clément Goubert
@clementgoubert.bsky.social

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

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.orgDfamOpen database of transposable elements and repetitive DNA families
Clément Goubert
@clementgoubert.bsky.social

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!

Clément Goubert reposted

plantgenomics.bsky.social
@plantgenomics.bsky.social

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

doi.orgLOCATE: using Long-read to Characterize All Transposable ElementsTransposons 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...
Clément Goubert
@clementgoubert.bsky.social

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

nature.comCrosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells - Nature GeneticsThe 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.
Clément Goubert
@clementgoubert.bsky.social

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

biorxiv.orgPannagram: unbiased pangenome alignment and the Mobilome callingPannagram 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...

Clément Goubert reposted

Alessandro Costa
@costalaboratory.bsky.social

I have received a Wellcome Discovery Award to study the initiation of eukaryotic DNA replication, with 8 years of funding at the Francis Crick Institute. Looking for a postdoc in molecular mechanisms, cryo-EM, cryo-FIB and in situ structure? Contact me now! 3 postdoc positions advertised soon.

Clément Goubert reposted

Fabien Burki
@fburki.bsky.social

Replying to @fburki.bsky.social

I would really appreciate a wide sharing of this post, as the candidate profile I am looking for is outside of my regular circle. Thank you so much. More info and how to apply here: uu.varbi.com/se/what:job/... (2/2)

uu.varbi.comPostdoktor inom i proteomik och eukaryotisk evolutionPostdoktor i proteomik och eukaryotisk evolution Detta projekt är en del av ett ERC Consolidator-anslag (PlastidOrigin) som tilldelats Fabien Burki och syftar till att studera en av de mest omvälvan