This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Poustka, A. J. Articles by Lehrach, H. Search for Related Content PubMed PubMed Citation Articles by Poustka, A. J. Articles by Lehrach, H. Social Bookmarking                   What's this?

Resources

Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters

¹ Evolution and Development Group, Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, 14195 Berlin, Germany ² Bioinformatics Group, Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, 14195 Berlin, Germany ³ Sequencing Group, Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, 14195 Berlin, Germany ⁴ California Institute of Technology, Division of Biology 156-29, Pasadena, California 91125, USA

Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also amenable to functional studies, the sea urchin system has emerged as one of the leading models for the analysis of the function of genomic regulatory networks that control development. We have analyzed a total of 107,283 cDNA clones of libraries that span the development of the sea urchin Strongylocentrotus purpuratus. Normalization by oligonucleotide fingerprinting, EST sequencing and sequence clustering resulted in an EST catalog comprised of 20,000 unique genes or gene fragments. Around 7000 of the unique EST consensus sequences were associated with molecular and developmental functions. Phylogenetic comparison of the identified genes to the genome of the urochordate Ciona intestinalis indicate that at least one quarter of the genes thought to be chordate specific were already present at the base of deuterostome evolution. Comparison of the number of gene copies in sea urchins to those in chordates and vertebrates indicates that the sea urchin genome has not undergone extensive gene or complete genome duplications. The established unique gene set represents an essential tool for the annotation and assembly of the forthcoming sea urchin genome sequence. All cDNA clones and filters of all analyzed libraries are available from the resource center of the German genome project at http://www.rzpd.de.

⁵ Corresponding author.
E-MAIL poustka{at}molgen.mpg.de; FAX 49-30-84131128.

[Supplemental material is available online at www.genome.org. All data described are deposited in a searchable online database available at http://www.molgen.mpg.de/ag_seaurchin/. All sequences described in this study have been submitted to the GenBank EST section under accession nos. CD289359-CD297607, CD303636-CD324638, and CD330178-CD342180.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				C. Rojas-Cartagena, P. Ortiz-Pineda, F. Ramirez-Gomez, E. C. Suarez-Castillo, V. Matos-Cruz, C. Rodriguez, H. Ortiz-Zuazaga, and J. E. Garcia-Arraras Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima Physiol Genomics, October 19, 2007; 31(2): 203 - 215. [Abstract] [Full Text] [PDF]

				R. E. Steele Genomics of Basal Metazoans Integr. Comp. Biol., August 1, 2005; 45(4): 639 - 648. [Abstract] [Full Text] [PDF]

				D. Groth, H. Lehrach, and S. Hennig GOblet: a platform for Gene Ontology annotation of anonymous sequence data Nucleic Acids Res., July 1, 2004; 32(suppl_2): W313 - W317. [Abstract] [Full Text] [PDF]