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Science 314 (5801): 960-962

Copyright © 2006 by the American Association for the Advancement of Science

The Transcriptome of the Sea Urchin Embryo

Manoj P. Samanta,1 Waraporn Tongprasit,2,3 Sorin Istrail,4,5 R. Andrew Cameron,5 Qiang Tu,5 Eric H. Davidson,5 Viktor Stolc2*

Abstract: The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.

1 Systemix Institute, Los Altos, CA 94024, USA.
2 NASA Ames Genome Research Facility, Moffet Field, CA 94035, USA.
3 Eloret Corporation, Sunnyvale, CA 94086, USA.
4 Brown University, Providence, RI 02912, USA.
5 California Institute of Technology, Pasadena, CA 91125, USA.

* To whom correspondence should be addressed. E-mail: vstolc{at}

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SpBase: the sea urchin genome database and web site.
R. A. Cameron, M. Samanta, A. Yuan, D. He, and E. Davidson (2009)
Nucleic Acids Res. 37, D750-D754
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cDNA Sequences for Transcription Factors and Signaling Proteins of the Hemichordate Saccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism.
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A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.
K. Hanada, X. Zhang, J. O. Borevitz, W.-H. Li, and S.-H. Shiu (2007)
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The Genome of the Sea Urchin Strongylocentrotus purpuratus.
Sea Urchin Genome Sequencing Consortium, E. Sodergren, G. M. Weinstock, E. H Davidson, R. A. Cameron, R. A. Gibbs, R. C. Angerer, L. M. Angerer, M. I. Arnone, D. R. Burgess, et al. (2006)
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