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Journal Articles (Data Paper) Cell Genomics Year : 2023

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

1 UCL - University College of London [London]
2 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
3 UMR 8030 - Génomique métabolique
4 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
5 MPI-MP - Max Planck Institute of Molecular Plant Physiology
6 Dahlem Center for Complex Quantum Systems & Fachbereich Physik
7 LBDV - Laboratoire de Biologie du Développement de Villefranche sur mer
8 IRBio UB - Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
9 SZN - Stazione Zoologica Anton Dohrn
10 EvoInside - LBDV_EVOINSIDE
11 abiocell - LBDV_ASCIDIAN_BIOCELL_GROUP
12 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
13 Okinawa Institute of Science and Technology Graduate University
14 University of Naples Federico II = Università degli studi di Napoli Federico II
15 IRIB - Istituto per la Ricerca e l’Innovazione Biomedica
16 IBV - Institut de Biologie Valrose
17 Institute for Biomedical Research and Innovation Palermo
18 Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Catalonia, Spain
19 LBTI - Laboratoire de Biologie Tissulaire et d'ingénierie Thérapeutique UMR 5305
20 ICREA - Institució Catalana de Recerca i Estudis Avançats
21 The Leon H. Charney School of Marine Sciences [Haifa]
22 IRIB - Institute for Research and Innovation in Biomedicine
23 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
24 BIOM - Biologie intégrative des organismes marins
Julie Poulain
Guy Lhomond
  • Function : Author
Maria Antonietta Ragusa
  • Function : Author
Vincenzo Cavalieri
  • Function : Author
Jenifer Croce
Maria Di Bernardo
  • Function : Author
Patrick Wincker
Thierry Lepage
  • Function : Author
  • PersonId : 1253065

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.
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Dates and versions

hal-04093287 , version 1 (10-05-2023)

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Ferdinand Marlétaz, Arnaud Couloux, Julie Poulain, Karine Labadie, Corinne da Silva, et al.. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. Cell Genomics, 2023, 3 (4), pp.100295. ⟨10.1016/j.xgen.2023.100295⟩. ⟨hal-04093287⟩
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