Paracentrotus lividus

The genome of an American sea urchin species, Strongylocentrotus purpuratus, has been sequenced and published in 2006 [1]. The size of the haploid genome is 810 Mb and about 23000 gene models have been predicted, values intermediate between those for the human (3.3 Gb / 30000 genes) and drosophila (180 Mb / 14000 genes) genomes.

Within the framework of the Network of Excellence “Marine Genomics Europe” (MGE) a group of 15 research teams from 7 European countries formed a consortium to develop genomic tools for the sea urchin Paracentrotus lividus. The first step focused on construction of several cDNAs and genomic libraries, the second is the current sequencing project carried out by Genoscope.

This project aims to generate a large DNA sequence database that will be used to study various aspects of embryo development. Topics covered by the participating laboratories include fertilization, egg activation, cell cycle control, regulation of translation, regulation of transcription, axis determination, early regionalisation, cell specification, cell migration, germ layers formation, ECM and cell adhesion, morphogenesis, cell signalling and gene regulatory networks.

Data generated by the project will be particularly useful to analyse gene regulatory networks involved in axis determination, cell fate specification and morphogenesis.

I. cDNA and genomic libraries built within or through the network.

I.1. cDNA libraries - Embryo cultures and RNA extraction from 8 embryonic stages (Villefranche-sur-Mer, T. Lepage). - Library construction and arraying (MPI Berlin - A. Poustka). 8 cDNA collections from different stages, size selected, amplified and pooled to construct and array 4 “full-length” libraries (vector pSPORT-SF1).

I.2. Genomic libraries
 Genomic DNA from sperm (I. Arnone, Naples)
 Short insert BAC library constructed by CalTech in pBACe3.6 (P. de Jong), average length 60 kb
 Long insert BAC library constructed for Garnet MGE by Bio S&T (Montreal) in pIndigoBAC-5 (Epicentre) 55296 clones, average length 135 kb

II. Sequencing projects conducted at Genoscope.

 140000 ESTs from arrayed cDNA libraries.
 More than 700 full-length cDNA sequences, selected from EST with a specific emphasis on transcription factors, signalisation and cell cycle regulators.
 Genomic sequence of about 50 selected genes, mainly transcription factors.

Contact: Patrick Wincker (Genoscope) - Christian Gache (Observatoire Océanologique - Villefranche/Mer)