Julie Poulain
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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: Tara Oceans (2009-2013) rDNA 16S V4V5 ASV table (DADA2) with nf-core/ampliseq 2.13
Tara Oceans (2009-2013) rDNA 16S V4V5 ASV table (DADA2) with nf-core/ampliseq 2.13 Open
This repository contains datasets describing the DADA2 ASVs generated from Tara Oceans 16S V4V5 rDNA data. The ASVs were generated using the nf-core workflow ampliseq. Please refer to the readme file (README.html) for more details.
View article: Genomics-based quantitative biogeography of marine plankton
Genomics-based quantitative biogeography of marine plankton Open
Marine plankton are key drivers of ocean productivity and global carbon cycling, yet their quantitative biogeography remains poorly characterized. Environmental genomic datasets are inherently compositional, restricting analyses to relativ…
View article: Tara Oceans (2009-2013) rDNA 18S V9 ASV table (DADA2) with nf-core/ampliseq 2.13
Tara Oceans (2009-2013) rDNA 18S V9 ASV table (DADA2) with nf-core/ampliseq 2.13 Open
This repository contains datasets describing the DADA2 ASVs generated from Tara Oceans 18S V9 rDNA data. The ASVs were generated using the nf-core workflow ampliseq. Please refer to the readme file (README.html) for more details.
View article: Tara Oceans (2009-2013) rDNA 18S V4 ASV table (DADA2) with nf-core/ampliseq 2.13
Tara Oceans (2009-2013) rDNA 18S V4 ASV table (DADA2) with nf-core/ampliseq 2.13 Open
This repository contains datasets describing the DADA2 ASVs generated from Tara Oceans 18S V4 rDNA data. The ASVs were generated using the nf-core workflow ampliseq. Please refer to the readme file (README.html) for more details.
View article: Phages with a broad host range are common across ecosystems
Phages with a broad host range are common across ecosystems Open
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: 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: 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: Water mass specific genes dominate the Southern Ocean microbiome
Water mass specific genes dominate the Southern Ocean microbiome Open
View article: High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits
High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits Open
View article: The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark <i>Scyliorhinus Canicula</i> Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates
The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark <i>Scyliorhinus Canicula</i> Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates Open
Cartilaginous fishes (chondrichthyans: chimeras and elasmobranchs -sharks, skates, and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic,…
View article: The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors
The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors Open
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: The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark<i>Scyliorhinus canicula</i>reveal the molecular bases of sensory organ evolution in jawed vertebrates
The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark<i>Scyliorhinus canicula</i>reveal the molecular bases of sensory organ evolution in jawed vertebrates Open
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic a…
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: The defensome of complex bacterial communities
The defensome of complex bacterial communities Open
Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system ( defensome ) encompasses a growing number of d…
View article: The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors
The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors Open
View article: Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean Open
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine mi…
View article: Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions
Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions Open
Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationsh…
View article: Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments
Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments Open
Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their nich…
View article: Predicting global distributions of eukaryotic plankton communities from satellite data
Predicting global distributions of eukaryotic plankton communities from satellite data Open
Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to ide…
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: Inter-comparison of marine microbiome sampling protocols
Inter-comparison of marine microbiome sampling protocols Open
Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodolo…
View article: Ocean-wide comparisons of mesopelagic planktonic community structures
Ocean-wide comparisons of mesopelagic planktonic community structures Open
For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of t…
View article: The defensome of complex bacterial communities
The defensome of complex bacterial communities Open
Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (or defensome ) encompasses a growing number of…
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
Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characteriz…
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