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Plividus_genome

ABSTRACT: Genome sequencing of the mediterranean sea urchin Paracentrotus lividus

PROVIDER: PRJEB25800 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR5621410_1.fastq.gz	Fastqsanger.gz
	ERR5621410_2.fastq.gz	Fastqsanger.gz
	ERR5621411_1.fastq.gz	Fastqsanger.gz
	ERR5621411_2.fastq.gz	Fastqsanger.gz

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A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus

Project description:Sea urchins lack proper eye organs but are photosensitive. In this study, we investigate an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus.

2022-09-20 | GSE211842 | GEO

Changes in the proteome of mediterranean sea urchin Paracentrotus lividus due to activation of its immune system

Project description:Our aim was to study the immune system of a Mediterranean sea urchin Paracentrotus lividus. Using a label free quantitative mass spectrometry approach we analyzed how bacterial lipopolysaccharide (LPS) is able to modulate the coelomocytes proteome and effect its cellular pathways such as cytoskeleton reorganization, stress and energetic homeostasis.

2020-01-30 | PXD008439 | Pride

Project description:Gonadal transcriptome of Mediterranean sea urchin (Paracentrotus lividus)

| PRJNA625933 | ENA

Comparative genomics of the sea urchin P. lividus highlights contrasting trends of genome and regulatory evolution in deuterostomes

Project description:Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of lineages through for instance the pmar1 and pop genes. Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.

2023-02-09 | GSE202034 | GEO

A molecular model of sea urchin reversible adhesion based on quantitative proteomics

Project description:Marine bioadhesives have unmatched performances especially in wet environments, being valuable sources of inspiration for industrial and biomedical applications. In sea urchins specialized adhesive organs, called tube feet, mediate adhesion. These are composed by a disc, which produces adhesive and de-adhesive secretions for strong reversible attachment, and a motile stem. After detachment, the secreted adhesive remains bound to the substratum as a footprint. Previous studies showed that sea urchin adhesive is composed of proteins and sugars, but so far only one protein, Nectin, was shown to be over-expressed as a transcript in tube feet discs, suggesting its involvement in sea urchin adhesion. Here we use high-resolution quantitative mass-spectrometry technologies to profile Paracentrotus lividus tube feet differential proteome, comparing protein expression levels in its adhesive part (disc) versus the non-adhesive part (stem). This allowed us to identify 163 highly over-expressed disc proteins and propose the first molecular model of sea urchin reversible adhesion. The secreted adhesive proteome was also analyzed, whereby we found that 70% of its components fall within five protein groups, involved in adhesive exocytosis and protection against microbes. Our data also provides evidence that Nectin is not only highly expressed in tube feet discs but is a component of the adhesive itself, thus constituting the first report of a sea urchin tube foot adhesive protein. These results give us an unprecedented insight on the molecular mechanics underlying sea urchins reversible adhesion, opening new doors to develop new, wet-reliable, reversible, efficient, ecological biomimetic adhesives.

2016-03-21 | PXD003122 | Pride

The sea urchin larval response to metaloxide nanoparticule exposure

Project description:Engineered nanoparticles (ENPs) are increasingly used to generate innovative industrial and medical goods. Because of their broad applications, they form a new class of pollutants with potential eco-toxicological impacts on marine ecosystems. Attempting to evaluate the risk, we investigated the toxicity of Iron and Zinc oxide ENPs on Paracentrotus lividus sea urchin embryos. Sea urchin embryos are sensitive to both ENPs with a much stronger impact of ZnO ENPs. Transcriptome-wide analyses were conducted after exposure to ENPs or the corresponding ions. Only a very limited number of genes are differentially expressed in response to Fe2O3 ENPs or FeCl3. In contrast, both ZnO ENPs and ZnSO4 caused alteration of biological processes with stronger perturbation of gene expression for the ionic form (higher LFC). Comparison of GO term enrichment of the differentially expressed genes indicated that ENP and ions elicited partly different mechanisms, suggesting that a nanoparticule-dependent response was induced. Remarkably, the expression of the metal binding and ROS scavenging Metallothioneins were massively induced by ZnO ENPs and ZnSO4 while ZnO ENPs and ions mainly repressed the transcription regulation processes which control embryo development.

2020-10-17 | GSE140784 | GEO

Floc'hlay2020 - SeaUrchin_model_ginsim

Project description:Multilevel logical model encompassing the Nodal and BMP pathways together with key transcription factors setting the dorsal-ventral axis in the sea urchin P. lividus embryo. This model accounts for the specification of wild-type ventral ectoderm, ciliary band and dorsal ectoderm, and further recapitulates sophisticated mutant phenotypes.

2021-01-06 | MODEL2002190001 | BioModels

sea urchin metagenome

Project description:Bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus

| PRJNA328923 | ENA

GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10025 Paracentrotus lividus

Project description:The outcomes of this project are to identify bioactive marine natural products from Irish marine life. This specific dataset contains LC-MS/MS spectra from tissue of the sea urchin Paracentrotus lividus. Files are part of the Metabolights dataset MTBLS874.

| MSV000090417 | GNPS

Paracentrotus lividus

Project description:Paracentrotus lividus transcriptome

| PRJNA375820 | ENA