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

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

PROVIDER: PRJNA834074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19034717_1.fastq.gz	Fastqsanger.gz
	SRR19034717_2.fastq.gz	Fastqsanger.gz
	SRR19034718_1.fastq.gz	Fastqsanger.gz
	SRR19034718_2.fastq.gz	Fastqsanger.gz
	SRR19034719_1.fastq.gz	Fastqsanger.gz

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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 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

coelomic P. lividus sea urchin microbiota

Project description:coelomic P. lividus sea urchin microbiota

| PRJEB27034 | ENA

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

Proteomic changes occurring along gonad maturation in the edible sea urchin Paracentrotus lividus

Project description:We report the proteomic characterization of gonads from wild P. lividus collected along coastal Sardinia, and describe the changes occurring in gonads according to sex and developmental stage. Gonads in the recovery, pre-mature, mature, and spent stages were analyzed using a shotgun proteomics approach based on filter-aided sample preparation followed by tandem mass spectrometry and label-free differential analysis. A detailed characterization of the proteome changes occurring in gonads of both sexes along maturation was achieved. Significant changes were seen in numerous proteins involved in nutrient accumulation and in gamete biology and maturation. Adding to an improved understanding of the P. lividus reproductive cycle in its natural environment, the results described in this work form the basis for defining novel protein markers and procedures for an easier sexing and staging, and for monitoring sea urchin gonad maturation in aquaculture plants.

2016-06-09 | PXD004200 | Pride

Analysis of the <i>P. lividus</i> sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes.

Project description:Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement.

| S-EPMC10112332 | biostudies-literature

Lipid metabolism of sea urchin Paracentrotus lividus in two contrasting natural habitats.

Project description:Sea urchins Paracentrotus lividus were harvested monthly from April 2015 to March 2016 from two sites in Sardinia (Italy). The two sites, a Posidonia oceanica meadow and a rocky bottom habitat, were naturally characterized by different food sources and availability, being mainly populated by the sea grass Posidonia oceanica and the brown algae Halopteris scoparia, respectively. Total lipids showed a minimum during winter in mature gonads, and a maximum in the summer (recovery stage). Fatty acid (FA) profiles of gut contents and gonads differed from those of the most available food sources. Levels of C18:3 (n-3) (ALA) discriminated samples from the two sites. Despite the very low amounts of C20:5 (n-3) (EPA) and C20:4 (n-6) (ARA) in P. oceanica, the main FA in gonads and gut contents were EPA and ARA in both sites. Increase in green algae intake prior to gametogenesis, especially C. cylindracea, likely affected EPA and ARA levels in gonads. The results show that P. lividus is able to concentrate lipids in gut contents and also to selectively store EPA, ARA and their precursors ALA and 18:2 (n-6) (LA). Moreover, bioconversion of ALA to EPA and of LA to ARA in P. lividus is suggested.

| S-EPMC8266866 | biostudies-literature

Paracentrotus lividus

Project description:RNA-seq data from Female and Male Mature Gonad samples from Paracentrotus lividus (Sea Urchin)

| PRJNA902773 | ENA

Agriornis lividus

Project description:Agriornis lividus

| PRJNA919576 | ENA

sea urchin metagenome

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

| PRJNA328923 | ENA