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

ABSTRACT: 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.

SUBMITTER: Marletaz F

PROVIDER: S-EPMC10112332 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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

Marlétaz Ferdinand F Couloux Arnaud A Poulain Julie J Labadie Karine K Da Silva Corinne C Mangenot Sophie S Noel Benjamin B Poustka Albert J AJ Dru Philippe P Pegueroles Cinta C Borra Marco M Lowe Elijah K EK Lhomond Guy G Besnardeau Lydia L Le Gras Stéphanie S Ye Tao T Gavriouchkina Daria D Russo Roberta R Costa Caterina C Zito Francesca F Anello Letizia L Nicosia Aldo A Ragusa Maria Antonietta MA Pascual Marta M Molina M Dolores MD Chessel Aline A Di Carlo Marta M Turon Xavier X Copley Richard R RR Exposito Jean-Yves JY Martinez Pedro P Cavalieri Vincenzo V Ben Tabou de Leon Smadar S Croce Jenifer J Oliveri Paola P Matranga Valeria V Di Bernardo Maria M Morales Julia J Morales Julia J Cormier Patrick P Geneviève Anne-Marie AM Aury Jean Marc JM Barbe Valérie V Wincker Patrick P Arnone Maria Ina MI Gache Christian C Lepage Thierry T

Cell genomics 20230405 4

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 <i>Paracentrotus lividus</i> 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 fas ...[more]

PMID: 37082140

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Project description:The sea urchin Paracentrotus lividus (Lamarck, 1816) is a keystone herbivore in the Mediterranean Sea due to its ability to transform macroalgal-dominated communities into barren areas characterized by increased cover of bare substrates and encrusting coralline algae, reduced biodiversity and altered ecosystem functions. P. lividus is also an excellent animal model for toxicology, physiology and biology investigations having been used for more than a century as a model for embryological studies with synchronously developing embryos which are easy to manipulate and analyze for morphological aberrations. Despite its importance for the scientific community, the complete genome is still not fully annotated. To date, only a few molecular tools are available and a few Next Generation Sequencing (NGS) studies have been performed. Here we aimed at setting-up an RNA extraction method to obtain high quality and sufficient quantity of RNA for NGS from P. lividus embryos at the pluteus stage. We compared five different RNA extraction protocols from four different pools of plutei (500, 1000, 2500 and 5000 embryos): TRIzol®, and four widely-used Silica Membrane kits, GenElute™ Mammalian Total RNA Miniprep Kit, RNAqueous® Micro Kit, RNeasy® Micro Kit and Aurum™ Total RNA Mini Kit. The quantity of RNA isolated was evaluated using NanoDrop. The quality, considering the purity, was measured as A260/A280 and A260/230 ratios. The integrity was measured by RNA Integrity Number (RIN). Our results demonstrated that the most efficient procedures were GenElute, RNeasy and Aurum, producing a sufficient quantity of RNA for NGS. The Bioanalyzer profiles and RIN values revealed that the most efficient methods guaranteeing for RNA integrity were RNeasy and Aurum combined with an initial preservation in RNAlater. This research represents the first attempt to standardize a method for high-quality RNA extraction from sea urchin embryos at the pluteus stage, providing a new resource for this established model marine organism.

Dataset Information

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

Publications

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

Similar Datasets

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