Jean-Marc Aury

🌊 Exploring the Ocean’s Genetic Secrets! Guided by @jm-aury.bsky.social and France Denoeud, @lafucarmen.bsky.social Doctoral Candidate at Genoscope - Centre National de Séquençage, shares how she's using long-reads on marine samples from the Tara Oceans expedition to explore genetic novelty.

ATLASea Mission – Day 6

In the dissection room, the final sampling steps are underway

🔬 Tissue fragments are collected, labeled, weighed, and logged into a data sheet for full traceability

❄️ Samples are flash-frozen in liquid nitrogen at -196°C to preserve DNA quality for sequencing at Genoscope

📸 ATLASea Mission – Day 4 - photography
Each selected specimen is individually photographed in the photo room by 3 dedicated teams.

🗂️ Images are paired with species sheets + unique ATLASea & MNHN labels to ensure full data traceability.

Next stop: the dissection room!
#MarineGenomics #Biodiversity

ATLASea has just launched a new sampling campaign in one of the most iconic sites of marine biodiversity.
For the next 10 days, our team of researchers will be working around the #Endoume_Marine_Station in Marseille to collect samples of marine species from the surrounding area.

🔍 ATLASea Mission – Day 3
Taxonomic experts examine each specimen, compare it to reference catalogs, and confirm ID - sometimes with help from global colleagues!

If the species is new to sequencing efforts, it’s selected (GO)
If not, it’s returned to the sea (NO GO)

#MarineBiodiversity #Fieldwork

@atlasea.bsky.social Sampling Day 2
Samples from the sea head straight to the wet lab for taxonomic grouping.

Dragged sediments are sieved and size-fractioned - revealing hidden benthic diversity.

Uncertain samples go into aquaria, then safely back to the sea if not selected.

#MarineBiodiversity

🐚 𝑳𝒊𝒎𝒂𝒓𝒊𝒂 Leads the Way — ATLASea Hits 1500 with a Mollusc That Claps! 🎉🎉

The #DIVE-Sea team has sampled the 1500th species for #ATLASea this week in Marseille!

𝑳𝒊𝒎𝒂𝒓𝒊𝒂 𝒕𝒖𝒃𝒆𝒓𝒄𝒖𝒍𝒂𝒕𝒂, a gorgeous bivalve mollusc of the family 𝐿𝑖𝑚𝑖𝑑𝑎𝑒, first described in 1792 by Giuseppe Olivi.

Struggling to find the tiny microchromosomes in draft bird genome assemblies?

Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...

🧵 below

(1/n)

@sangerinstitute.bsky.social

1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata.
It uses a colored de Bruijn graph under the hood.

This week, ATLASea is in the Endoume marine station from @univ-amu.fr for a new sampling expedition focused on fish and some additional species! The team has already collected 30 new species.
In the lab, our colleagues Caroline, Janaina and Morgane sampling tissues from a coral.
#MarineBiodiversity

Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function | Microbiology Spectrum Vast oceanic regions are nutrient-poor, yet several microalgae thrive in these environments. While various acclimation strategies to these conditions have been discovered in a limited number of model microalgae, many important lineages remain ...

New paper using 2 RCC Pelagomonas strains, co-authored by 2 members of the RCC, Pris and Ian.

journals.asm.org/doi/10.1128/...

It's finally out!!!! Our review on long-reads transcriptomics was published in @natrevgenet.bsky.social!! You can have a look at the paper here rdcu.be/efugl! We hope you like it 😀

📢 #PhD and #postdoctoral positions available in Pedro Oliveira lab. We seek candidates for Microbial Genomic and Epigenetic teams to work on #epigenomics of #bacteria and #microbiomes. Start: Fall 2025.
Please RT!

@cea.fr @univparissaclay.bsky.social @genopole.bsky.social @upcite.bsky.social

If you are looking for published plant genomes www.plabipd.de/pubplant_mai... might be useful where Rainer is tracking species with genomes for almost 10 years now... time flies. As he has added new useful views, we thought it is time to summarize this. www.biorxiv.org/content/10.1...

Genus-wide plant pangenome could inform next-generation crop design A pangenome for the genus Solanum.

Genus-wide plant pangenome could inform next-generation crop design

www.nature.com/articles/d41...

ATLASea : plus de 1000 espèces marines collectées en 2024 ! Un an après son lancement, le programme ATLASea, progresse vers son objectif de séquencer les génomes d’espèces marines.

🌊🔬 ATLASea : bilan exceptionnel en 2024 !

Plus de 1000 espèces marines collectées lors des campagnes océanographiques du PEPR ATLASea en Nouvelle-Calédonie, à Dinard, dans la Manche et en Guadeloupe ! 🐠🦑

🤝 @atlasea.bsky.social @cea.fr
➡️ Plongez dans cette aventure scientifique

Coral venom and toxins as protection against crown-of-thorns sea star attack https://www.biorxiv.org/content/10.1101/2025.02.10.637440v1

For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...

https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/

🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!

From 17/01 to 8/02, the International Bottom Trawl Survey 🚢 (IBTS) Mission 🌊 🎣 is underway, to assess commercial fish stocks in the North Sea
🔎 #DIVE-Sea team from ATLASea, coordinated by Elio Raphalen #Ifremer, is joining the mission for the first 3 days to collect new marine specimens in this area

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Did you know our colleagues have been working tirelessly on a new #Ensembl genome browser? 🥳 Join us at this @ebi.embl.org webinar to learn more about the new browser and how to navigate it 🧬 💻

Registration is free but essential

📆 Wed, 29 Jan 2025
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ℹ bit.ly/EnsBeta

Attention people of Bluesky! Today, we had a double celebration. Alejandro has gotten his paper published #ConesaLab 🧑‍🔬 genome.cshlp.org/content/earl...

Vincent Colot, héraut de l’épigénétique des plantes Le généticien des plantes, directeur de recherche au CNRS, explore le rôle de l’épigénétique à travers le monde végétal depuis plus de vingt-cinq ans. A l’orée de la retraite, il continue de chercher ...

[fr] Vincent Colot, héraut de l’épigénétique des plantes
www.lemonde.fr/sciences/art...

Richard Cordeaux (EGCE lab, Gif sur Yvette, France) is offering an 18-month postdoc position in evolutionary genomics to study sex determination and resistance to vertical transmission of feminizing Wolbachia endosymbionts in an isopod. #SymbioSky #Wolbachia

filesender.renater.fr?s=download&t...

Origin of metazoans Roscoff (Bretagne), France, June 16-20, 2025Deadline for application: March 4, 2025

Monod Conference "Origin of metazoans": fossils, genomes, cell biology, gene regulation, development, and more.

Join us in Roscoff for an exceptional speaker line-up and stunning venue!

🗓️Abstract deadline: March 4.

Register and share!
www.insb.cnrs.fr/fr/origin-me...

Curious about alternative splicing? Kick off the year with our latest review in COSB! authors.elsevier.com/sd/article/S...

Mumemto: efficient maximal matching across pangenomes Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

@conesalab.bsky.social @i2sysbio.bsky.social presents their tool PaintOmics4. It is a web-based tool for the integrative analysis and interpretation of multiomics data. Follow the online seminar at us06web.zoom.us/j/88518061453on January 15th at 11:00 CET

In the coming years, thanks to the @atlasea.bsky.social program, we should be able to generate more chromosome-scale assemblies of brown algae. Stay tuned!

Data available on the brown algae portal:
phaeoexplorer.sb-roscoff.fr