The PR2 database

The PR2 database

@pr2-database.bsky.social

PR2 is a set of three interconnected sequence public databases focusing on protist taxonomic groups: a reference sequence database (pr2), a primer database (pr2-primers) and a metabarcode database (metapr2). https://pr2-database.org/

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The PR2 database
@pr2-database.bsky.social

Using the PR2 database...

Evgenii Protasov@evgenii-protasov.bsky.social

Half of microbial eukaryote literature focuses on only twelve human parasites #microbiology #protists #eukaryotes @isme-microbes.bsky.social academic.oup.com/ismej/articl...

academic.oup.comHalf of microbial eukaryote literature focuses on only 12 human parasitesAbstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc
The PR2 database
@pr2-database.bsky.social

Version 5.1.1 of the PR2 database has been released. The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations

doi.orgA novel taxonomic database for eukaryotic mitochondrial cytochrome oxidase subunit I gene (eKOI), with a focus on protists diversityAbstract. Metabarcoding has emerged as a robust method for assessing biodiversity patterns by retrieving environmental DNA directly from ecosystems. While
The PR2 database
@pr2-database.bsky.social

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

Javier del Campo@fonamental.bsky.social

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 🙏

The PR2 database
@pr2-database.bsky.social

A paper using the PR2 and metaPR2 database.

Adriana Lopes@lopessantosadriana.bsky.social

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...

The PR2 database reposted

Anthony M. Bonacolta
@ambonacolta.bsky.social

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

The PR2 database@pr2-database.bsky.social

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:

The PR2 database reposted

Anders K. Krabberød
@krabberod.bsky.social

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

- 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

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

The PR2 database
@pr2-database.bsky.social

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

Vasily Zlatogursky@zlatogursky.bsky.social

@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

The PR2 database
@pr2-database.bsky.social

New paper using PR2.

Daniel Vaulot@daniel-vaulot.bsky.social

New paper with Norwegian colleagues. Thanks for inviting me to participate... And published by Canadian Science... cdnsciencepub.com/doi/full/10....

cdnsciencepub.comThe community of marine alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth, and water massThe 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...
The PR2 database
@pr2-database.bsky.social

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

Alexis Stamatakis@stamatak.bsky.social

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...

biorxiv.orgraxtax: A k-mer-based non-Bayesian Taxonomic ClassifierTaxonomic 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...

The PR2 database reposted

Alexis Stamatakis
@stamatak.bsky.social

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...

biorxiv.orgraxtax: A k-mer-based non-Bayesian Taxonomic ClassifierTaxonomic 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...
The PR2 database
@pr2-database.bsky.social

A tool to use with the metaPR2 datasets ?

Amy D Willis@amydwillis.bsky.social

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...

The PR2 database
@pr2-database.bsky.social

Very interesting paper #usingPR2

Kenneth Dumack@dumack.bsky.social

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:

The PR2 database
@pr2-database.bsky.social

This very interesting Nature paper uses the metaPR2 database to assess the distribution of DPH containing diatoms.

Angela Falciatore@afalciat.bsky.social

Excited to share this work from our lab @IBPC and collaborators! Thanks to diatoms, some of the mysteries surrounding phytochrome photoreceptors in the oceans are beginning to be unraveled! Phytochrome remains the "pigment of imagination’ Congratulations to all the authors! doi.org/10.1038/s415...

The PR2 database reposted

Javier del Campo
@fonamental.bsky.social

Happy to be part of this effort led by Rubén González-Miguéns: A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI) https://www.biorxiv.org/content/10.1101/2024.12.05.626972v1 eKOI will be integrated into @pr2-database.bsky.social 🙌 #protistsonsky

biorxiv.orgA Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analysesMetabarcoding has emerged as a robust method for understanding biodiversity patterns by retrieving environmental DNA (eDNA) directly from ecosystems. Its low cost and accessibility have extended its…
The PR2 database
@pr2-database.bsky.social

#usingpr2

Anthony M. Bonacolta@ambonacolta.bsky.social

🚨New Preprint🚨: A Single-cell Atlas of Coral Bleaching! 🪸🦠🔥. We show the microbial ecology of coral bleaching from the gene expression of host and symbiont cells to the shifts in the bacterial and protist communities within the holobiont! #ProtistsOnSky #SymbioSky #MicroSky 🧪

researchsquare.comA Single-Cell Atlas of Coral BleachingThe symbiosis between corals and dinoflagellate algae is disrupted by heat stress, leading to bleaching. Recurring bleaching events, driven by the climate crisis, are causing massive coral mortality a...