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The PR2 database @pr2-database.bsky.social · 1d

More info here: pr2database.github.io/metapr2-shin...

pr2database.github.io

The PR2 database @pr2-database.bsky.social · 1d

metaPR2 version 3.0 has just been released.

Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.

app.metapr2.org

MetaPR2

app.metapr2.org

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The PR2 database @pr2-database.bsky.social · Jun 29

Javier is the co-coordinaror of PR2... Warn congratulations.

Javier del Campo @fonamental.bsky.social · Jun 27

It is an honor to receive the #ISOP Hutner Award to a researcher within 15 years of his PhD who has made outstanding contributions in protistology 😊

I would like to thank my mentors (Ramon Massana, @multicellgenome.bsky.social, @pjkeelinglab.bsky.social) and my past and present students 🙏

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The PR2 database @pr2-database.bsky.social · Jun 28

A paper using the PR2 and metaPR2 database.

Adriana Lopes @lopessantosadriana.bsky.social · Jun 24

What’s thriving under Arctic sea ice? We tracked photosynthetic protists during the Arctic UIB,revealing a shift from polar to polar-temperate taxa & spotlighting overlooked groups!Great team & Dr. Sim effort! @biovitenskap.bsky.social @roscoff-collection.bsky.social academic.oup.com/ismecommun/a...

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The PR2 database @pr2-database.bsky.social · May 7

Nice paper making use of PR2

Johan Renaudie @plannapus.bsky.social · May 7

Now published online in Current Biology! www.cell.com/current-biol...

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Reposted by The PR2 database

Håvard Kauserud @drhyfe.bsky.social · Apr 10

@daniel-vaulot.bsky.social presenting the @pr2-database.bsky.social at our DNA metabarcoding course at @biovitenskap.bsky.social A very good new addition to our biannual course 👏

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Reposted by The PR2 database

Anthony M. Bonacolta @ambonacolta.bsky.social · Apr 3

Grateful I got the opportunity to contribute to this amazing resource #ProtistsOnSky

The PR2 database @pr2-database.bsky.social · Apr 3

Announcing the new release of the PR2 database, version 5.1.
pr2-database.org/post/news/20...

Very big thanks to all the contributors: @fonamental.bsky.social @ambonacolta.bsky.social @krabberod.bsky.social and more...

A few highlights:

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Reposted by The PR2 database

Anders K. Krabberød @krabberod.bsky.social · Apr 3

I am very happy that ROD (The Ribosomal Operon Database) is now included in the outstanding PR2 web interface, enhancing its accessibility and utility. I hope to make some updates to ROD in the near future. with @drhyfe.bsky.social

The PR2 database @pr2-database.bsky.social · Apr 3

- The web interface now provides access to the ROD database that contains full-length eukaryotic ribosomal operons developed by @krabberod.bsky.social

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The PR2 database @pr2-database.bsky.social · Apr 3

Please report any issue here:
github.com/vaulot/pr2_d...

Issues · pr2database/pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database

github.com

The PR2 database @pr2-database.bsky.social · Apr 3

Some functional traits have been added:

- HAB (Harmful Algal Bloom) species
- ecological function - from Sommeria-Klein et al. 2021

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The PR2 database @pr2-database.bsky.social · Apr 3

A few taxonomic groups have been updated from work performed during the 2023 Barcelona EukRef workshop and from individual contributions including:

- Picozoa
- Choropicophyceae
- Rhodophyta
- Dinophyceae
- Foraminifera

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The PR2 database @pr2-database.bsky.social · Apr 3

- The web interface now provides access to the ROD database that contains full-length eukaryotic ribosomal operons developed by @krabberod.bsky.social

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The PR2 database @pr2-database.bsky.social · Apr 3

Announcing the new release of the PR2 database, version 5.1.
pr2-database.org/post/news/20...

Very big thanks to all the contributors: @fonamental.bsky.social @ambonacolta.bsky.social @krabberod.bsky.social and more...

A few highlights:

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The PR2 database @pr2-database.bsky.social · Apr 2

Please let us know of any problem here: github.com/pr2database/...

Issues · pr2database/pr2database

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database - Issues · pr2database/pr2database

github.com

1

The PR2 database @pr2-database.bsky.social · Apr 2

We are back on-line. It took less time than anticipated to upgrade R....

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The PR2 database @pr2-database.bsky.social · Apr 2

The PR2, metaPR2 and PR2-primers websites will be off in the coming days as we are switching from R 3.6 to R 4.4.

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The PR2 database @pr2-database.bsky.social · Mar 28

Protists are not just sequences, they have incredible shapes...

Vasily Zlatogursky @zlatogursky.bsky.social · Mar 28

@amoebadiscovery.bsky.social made an iteresting interview with me about #heliozoa and #centrohelids - I think these organisms are really important, understudied and gorgeous 😍 Also lots other intresting reading and beatiful pictures! #protistsonsky link: tinyurl.com/adiscovery1

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The PR2 database @pr2-database.bsky.social · Mar 26

New paper using PR2.

Daniel Vaulot @daniel-vaulot.bsky.social · Mar 26

New paper with Norwegian colleagues. Thanks for inviting me to participate... And published by Canadian Science...

cdnsciencepub.com/doi/full/10....

The community of marine alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth, and water mass

The marine alveolates (MALVs) are a highly diverse group of parasitic dinoflagellates, which may regulate populations of a wide range of hosts, including other dinoflagellates, copepods, and fish eggs...

cdnsciencepub.com

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The PR2 database @pr2-database.bsky.social · Mar 20

Looks like a very good tool to use with the PR2 database.

Alexis Stamatakis @stamatak.bsky.social · Mar 19

Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier

Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...

www.biorxiv.org

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Reposted by The PR2 database

Alexis Stamatakis @stamatak.bsky.social · Mar 19

Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier

Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...

www.biorxiv.org

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The PR2 database @pr2-database.bsky.social · Mar 14

A tool to use with the metaPR2 datasets ?

Amy D Willis @amydwillis.bsky.social · Mar 14

We've just released radEmu v2.0.0 🥳🦤😻

`remotes::install_github("statdivlab/radEmu")`

A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!

Release notes: github.com/statdivlab/r...

A screenshot of the release notes for radEmu v2. Text available at https://github.com/statdivlab/radEmu/releases

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The PR2 database @pr2-database.bsky.social · Mar 1

All PR2 shiny servers are back up and running...

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Reposted by The PR2 database

Daniel Vaulot @daniel-vaulot.bsky.social · Feb 27

From the Richter lab in Barcelona... new species are always exciting...

Roscoff Culture Collection @roscoff-collection.bsky.social · Feb 27

New goniomonad genus and species with strains deposited in the Roscoff Culture Collection

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

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Reposted by The PR2 database

Daniel Vaulot @daniel-vaulot.bsky.social · Feb 28

Join a world renowned marine lab in France.

New Junior Professor Chair (CPJ) opened in the Biological Station in Roscoff. The position is focused on the ecological, evolutionary, and functional roles of marine fungi, crucial to understanding our oceans.

www.sb-roscoff.fr/fr/2025/02/2...

Open position Junior Professor Chair (CPJ)

Open position Junior Professor Chair (CPJ) 2025. CNRS EE-BIO

www.sb-roscoff.fr

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The PR2 database @pr2-database.bsky.social · Feb 7

Very interesting paper #usingPR2

Kenneth Dumack @dumack.bsky.social · Feb 4

Have you used #network_analyses in the past to analyse your #ecology data? Have you wondered how many of those correlations actually represent interactions between #microorganisms? Here I present a paper how we leveraged #protistsonsky to evaluate the validity of the method. A thread: