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View article: Tara Pacific CDIV ITS2 Symbiodiniaceae data release V2
Tara Pacific CDIV ITS2 Symbiodiniaceae data release V2 Open
This data is the result of the primary analysis of the ITS2 sequencing data associated with the Coral Diversity dataset collected from all islands as part of the Tara Pacific expedition. A full README is contained within the data upload. I…
View article: From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding
From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding Open
In the last decades, environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecological patterns across time and space. …
View article: The JEDI marker as a universal measure of planetary biodiversity
The JEDI marker as a universal measure of planetary biodiversity Open
Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hinderi…
View article: From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding
From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding Open
In the last decades environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecological patterns across time and space. W…
View article: SnS2-TiO2 Heterojunction Designed for Reductive Degradation of Contaminants of Emerging Concern
SnS2-TiO2 Heterojunction Designed for Reductive Degradation of Contaminants of Emerging Concern Open
Contaminants of emerging concern (CECs), including pharmaceuticals and perfluorinated compounds, pose a growing threat to water quality due to their persistence and resistance to conventional treatment methods. In this context, photocataly…
View article: Morphological traits and machine learning for genetic lineage prediction of two reef-building corals
Morphological traits and machine learning for genetic lineage prediction of two reef-building corals Open
Integrating multiple lines of evidence that support molecular taxonomy analysis has proven to be a robust method for species delimitation in scleractinian corals. However, morphology often conflicts with genetic approaches due to high phen…
View article: Is the Gelatinous Matrix of Nassellaria (Radiolaria) a Strategy for Coping With Oligotrophy?
Is the Gelatinous Matrix of Nassellaria (Radiolaria) a Strategy for Coping With Oligotrophy? Open
Radiolaria are heterotrophic protists abundant in the world's oceans, playing important roles in biogeochemical cycles. Some host photosynthetic algae, contributing to primary production. Such mixotrophic behaviour is believed to explain t…
View article: First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples
First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Open
The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites,…
View article: Emergent patterns of patchiness differ between physical and planktonic properties in the ocean
Emergent patterns of patchiness differ between physical and planktonic properties in the ocean Open
View article: First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples
First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Open
The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory among designated European coastal marine sites, s…
View article: Genome-resolved diversity and biosynthetic potential of the coral reef microbiome
Genome-resolved diversity and biosynthetic potential of the coral reef microbiome Open
Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services. They are also reservoirs of bioactive compounds, many of which are produced by microbial symbionts associated with reef invertebrate hosts. Howev…
View article: DNA extraction from environmental size-fractionned plankton samples v1
DNA extraction from environmental size-fractionned plankton samples v1 Open
This protocol has been designed for total DNA extraction from environmental marine water samples. Samples from different plankton size fractions are collected by Niskin bottles (Step Case 1) or by plankton net tows (Step Case 2) and are fi…
View article: Single-cell transcriptomics highlights sexual cues among reproductive life stages of uncultivated Acantharia (Radiolaria)
Single-cell transcriptomics highlights sexual cues among reproductive life stages of uncultivated Acantharia (Radiolaria) Open
As an innate property of life, the ability to reproduce is a key process for the perpetuation of organisms. Along the evolution of protist reproductive strategies, the molecular machinery of sexual recombination is estimated to have been i…
View article: rDNA 18S V9 ASV tables (SWARM) for Tara Pacific Expedition
rDNA 18S V9 ASV tables (SWARM) for Tara Pacific Expedition Open
This data is the result of the second analysis of the V9 18S rDNA metabarcoding sequencing data from the Tara Pacific expedition. The analysis was conducted using cutadapt, vsearch, swarm and lulu. Please refer to the readme file for more …
View article: Gelatinous matrix, an original strategy to cope with oligotrophy in Nassellaria (Radiolaria)
Gelatinous matrix, an original strategy to cope with oligotrophy in Nassellaria (Radiolaria) Open
Radiolaria are heterotrophic protists abundant in the world’s oceans playing important roles in biogeochemical cycles. Some species host photosynthetic algae also contributing to primary production. Such mixotrophic behaviour is believed t…
View article: Single-Cell Transcriptomics Highlights Sexual Cues Among Reproductive Life Stages of Uncultivated Acantharia (Radiolaria)
Single-Cell Transcriptomics Highlights Sexual Cues Among Reproductive Life Stages of Uncultivated Acantharia (Radiolaria) Open
View article: Nucleic acids extraction from single cell using MasterPure Complete DNA purification (Epicenter) v2
Nucleic acids extraction from single cell using MasterPure Complete DNA purification (Epicenter) v2 Open
Radiolaria are protists which can't be cultivated. These microoganisms have to be isolated by single-cell for genetic identification and it can be difficult to get clean DNA. Here we optimized a DNA extraction protocol from protist single-…
View article: Tara Pacific Biomarker-Based Coral Phenotype Data Release - Pocillopora
Tara Pacific Biomarker-Based Coral Phenotype Data Release - Pocillopora Open
Those data correspond to the measurements of the phenotype signatures of Pocillopora colonies collected through 30 Pacific Islands. More precisely, six different biomarkers have been measured for each colony: Animal biomass, Symbiont bioma…
View article: RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel) v2
RNA/DNA extraction from plankton natural samples using NucleoSpin RNA + RNA/DNA Buffer kits (Macherey Nagel) v2 Open
This protocol has been developped for simultaneous nucleic acid (RNA and DNA) extraction from environmental water samples collected by filtration on polycarbonate 47mm and 142mm filters. It has been developped during BioMarks project (2009…
View article: SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2)
SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2) Open
This repository contains a rDNA 18S V4 ASV table (astan-18sv4_dada2_v1.0.filtered.table.with.taxo.lulu.tsv.gz) for SOMLIT-Astan time-series (2009-2016). Each ASV, one per row, is described by the following fields: amplicon = ASV identifier…
View article: SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2)
SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2) Open
This repository contains a rDNA 18S V4 ASV table (astan-18sv4_dada2_v1.0.filtered.table.with.taxo.lulu.tsv.gz) for SOMLIT-Astan time-series (2009-2016). Each ASV, one per row, is described by the following fields: amplicon = ASV identifier…
View article: Seasonal dynamics of a glycan‐degrading flavobacterial genus in a tidally mixed coastal temperate habitat
Seasonal dynamics of a glycan‐degrading flavobacterial genus in a tidally mixed coastal temperate habitat Open
Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonisation by macroalgae that mostly store carbon as glycans, contributing substantiall…
View article: Different environmental response strategies in sympatric corals from Pacific Islands
Different environmental response strategies in sympatric corals from Pacific Islands Open
View article: Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation
Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation Open
View article: Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals
Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals Open
View article: Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems
Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems Open
View article: Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean
Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean Open
View article: Diversity of the Pacific Ocean coral reef microbiome
Diversity of the Pacific Ocean coral reef microbiome Open
View article: Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean
Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean Open
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remai…
View article: Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes Open