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

Poustka, Albert J. and Groth, Detlef and Hennig, Steffen and Thamm, Sabine and Cameron, Andrew and Beck, Alfred and Reinhardt, Richard and Herwig, Ralf and Panopoulou, Georgia and Lehrach, Hans (2003) Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters. Genome Research, 13 (12). pp. 2736-2746. ISSN 1088-9051. http://resolver.caltech.edu/CaltechAUTHORS:20121023-162305381

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Abstract

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.


Item Type:Article
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URLURL TypeDescription
http://dx.doi.org/10.1101/gr.1674103 DOIUNSPECIFIED
http://genome.cshlp.org/lookup/doi/10.1101/gr.1674103PublisherUNSPECIFIED
Additional Information:© 2003 Cold Spring Harbor Laboratory Press. Received July 19, 2003; accepted in revised form September 11, 2003. We thank Matthew Clark, Pia Aanstad, Georg Otto, and Carola Burgtorf for discussions in the course of this project and Anahid Powell and Brian Cusack for help on the manuscript. We thank the RZPD for support with DNA filter production and Mario Drungowski for help with image analysis. This work was supported by the Max Planck Gesellschaft zur Förderung der Wissenschaften e.v. A.C. and larval library construction was supported by US NSF grant IBN-9982875. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
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Max Planck Gesellschaft zur Förderung der WissenschaftenUNSPECIFIED
NSFIBN-9982875
Record Number:CaltechAUTHORS:20121023-162305381
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20121023-162305381
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:35056
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:24 Oct 2012 18:30
Last Modified:03 Sep 2014 04:29

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