Julie Poulain

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

The paper characterizes the eukaryotic diversity in coral reef environments, revealing high diversity and identifying environmental drivers shaping these communities.

HIDDEN APICOMPLEXAN PARASITE DIVERSITY LINKS CORAL AND PLANKTON MICROBIOMES ACROSS REEF SEASCAPES

The paper investigates the diversity and distribution of Apicomplexa across marine environments using metabarcoding data, revealing previously unknown diversity and biogeographic patterns.

Ocean-scale transcriptomic analysis of corallicolids (Apicomplexa) reveals their ubiquity and molecular interactions with Pocillopora corals.

The paper analyzes corallicolid parasites in Pocillopora corals across the Pacific Ocean, finding their widespread presence and linking their abundance to environmental factors and host immune responses.

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

This study assesses the microbial biosynthetic potential of reef-building corals using genome-resolved metagenomics, revealing host-specific microbiomes with high biotechnological value.

Genomics-based quantitative biogeography of marine plankton

This study generates absolute estimates of plankton cell concentrations and carbon biomass using environmental genomic data, revealing ecological associations and quantitative biogeographies of photosynthetic lineages.

The JEDI marker as a universal measure of planetary biodiversity

The paper introduces the JEDI marker as a universal biodiversity measure, demonstrating its applicability across ecological scales and providing an automated bioinformatic workflow for standardized analysis.

Emergent patterns of patchiness reflect decoupling between ocean physics and biology

The paper analyzes global ocean data to show that physical and biological patchiness are decoupled, using variance slope to quantify spatial patterns.

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

The defensome of complex bacterial communities

The paper analyzes defensomes in 7,759 bacterial genomes from diverse environments, revealing variation in defense systems linked to lifestyle and habitat.

Disparate patterns of genetic divergence in three widespread corals across a pan-Pacific environmental gradient highlights species-specific adaptation trajectories.

The paper analyzes genetic divergence in three coral species across a Pacific environmental gradient, showing species-specific evolutionary patterns despite similar environments.

Pervasive tandem duplications and convergent evolution shape coral genomes

The paper reports higher gene counts in two coral genomes due to tandem duplications, suggesting a role in immune system and disease resistance.

Male differentiation in the marine copepod Oithona nana reveals the development of a new nervous ganglion linked to Lin12-Notch-Repeat protein-associated proteolysis

The paper identifies male-specific nervous ganglia and LDPGs in Oithona nana, linking them to proteolysis and male-specific physiology.

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

The paper uses dual RNAseq to study the kinetics of skin microbiome and host response to T. maritimum infection in fish, finding immune gene upregulation in resistant individuals.

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

The paper develops a flexible metabarcoding pipeline for prokaryotic and eukaryotic data, showing clustering and LULU-curation improve biodiversity inventory reliability.

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

This paper develops a field-friendly framework for characterizing coral holobionts using nanopore sequencing and bioinformatics pipelines, revealing reef-scale bacterial networks and host-specific associations.

An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities

This study evaluates eDNA metabarcoding protocols for deep-sea biodiversity, finding that DNA is more reliable than RNA and larger sediment samples improve accuracy.

Proteolysis and neurogenesis modulated by LNR domain proteins explosion support male differentiation in the crustacean Oithona nana

The paper investigates sexual dimorphism in Oithona nana by analyzing transcriptomic and protein-protein interaction data, finding male-specific enrichment in LNR domain proteins and pathways related to proteolysis and neurogenesis.

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

The paper analyzes global ocean viruses to uncover their genomic diversity and ecological roles in biogeochemical cycles.