MPIMG - Evolution and Development, the paracentrotus lividus database (2007)

Evolutionary Systems Biology of the Sea urchin

The Sea urchin is a well-recognized model organism used in embryological studies since over a century. The genome of S.purpuratus has been sequenced at Baylor College of Medicine in U.S., (Science 2006 Nov 10;314(5801):941-52 [1]) , while through the EU funded Network of Excellence Marine Genomics (NoEMG) programme funds were obtained to create genomic resources for an additional sea urchin species the mediterranean urchin Paracentrotus lividus. This underlines the increasing significance that the sea urchin system is gaining. 4 cDNA were libraries generated within NoEMG. One from unfertilized eggs (Pl_EGG), one from a pool of cleavage and early blastula stage (Pl_CLEB), one from a pool of mid and swimming blastula stage (Pl_MBSB) and one of a gastrula and pluteus stage (Pl_GASPLU). Each library consists of 110.592 clones, which have been arrayed and printed on nylon macroarrays for screening purposes. All clones and filters are available through imagenes http://www.imagenes-bio.de [2]). A total of 141.909 ESTs were generated resulting in 29.589 independent sequence clusters. To complement the gene representation to a later stage of development and identify additional genes we generated 90.929 454 reads of 4 weeks larva. These could be clustered into 28.969 independent clusters using the novartis newbler assembler. A co-assembly of EST and 454 data (a total of 232.838 reads) resulted in 41.127 independent sequence items. The Pliv database offers many options to explore this sequence data. Among other options it is possible to search Pliv genes via the gene (glean3) predictions from the genome of S.purpuratus. Please read the Help page for instructions.

The Paracentrotus lividus Genome Initiative

The Sea Urchin Group from Marine Genomics Europe, the Institut de la Genomique Marine and Genoscope :

Arnone, M.I., Branno, M., Ciapa, B., Cormier, C., Di Bernardo, M., Di Carlo, M., Dossat, C., Flytzanis, C., Gache, C., Geneviere, A.M., Lepage, T., Martinez, P., Matranga, V., Poulain, J., Poustka, A.J., Schupp, I., Thorndyke, M., Wellenreuther, R., Wincker, P.

Genomics Research MPIMG - Evolution and Development, the paracentrotus lividus database (2007)
Intro Search Gene Ontology Blast Help Seaurchin DB Ciona DB	Evolutionary Systems Biology of the Sea urchin The Sea urchin is a well-recognized model organism used in embryological studies since over a century. The genome of S.purpuratus has been sequenced at Baylor College of Medicine in U.S., (Science 2006 Nov 10;314(5801):941-52 [1]) , while through the EU funded Network of Excellence Marine Genomics (NoEMG) programme funds were obtained to create genomic resources for an additional sea urchin species the mediterranean urchin Paracentrotus lividus. This underlines the increasing significance that the sea urchin system is gaining. 4 cDNA were libraries generated within NoEMG. One from unfertilized eggs (Pl_EGG), one from a pool of cleavage and early blastula stage (Pl_CLEB), one from a pool of mid and swimming blastula stage (Pl_MBSB) and one of a gastrula and pluteus stage (Pl_GASPLU). Each library consists of 110.592 clones, which have been arrayed and printed on nylon macroarrays for screening purposes. All clones and filters are available through imagenes http://www.imagenes-bio.de [2]). A total of 141.909 ESTs were generated resulting in 29.589 independent sequence clusters. To complement the gene representation to a later stage of development and identify additional genes we generated 90.929 454 reads of 4 weeks larva. These could be clustered into 28.969 independent clusters using the novartis newbler assembler. A co-assembly of EST and 454 data (a total of 232.838 reads) resulted in 41.127 independent sequence items. The Pliv database offers many options to explore this sequence data. Among other options it is possible to search Pliv genes via the gene (glean3) predictions from the genome of S.purpuratus. Please read the Help page for instructions. The Paracentrotus lividus Genome Initiative The Sea Urchin Group from Marine Genomics Europe, the Institut de la Genomique Marine and Genoscope : Arnone, M.I., Branno, M., Ciapa, B., Cormier, C., Di Bernardo, M., Di Carlo, M., Dossat, C., Flytzanis, C., Gache, C., Geneviere, A.M., Lepage, T., Martinez, P., Matranga, V., Poulain, J., Poustka, A.J., Schupp, I., Thorndyke, M., Wellenreuther, R., Wincker, P.
Programming: Detlef Groth Data: Albert Poustka