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Integrative and Comparative Biology Advance Access published online on June 3, 2006
Integrative and Comparative Biology, doi:10.1093/icb/icl007
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oxfordjournals.org.

Genomic and Proteomic Approaches in Crustacean Biology

Construction and characterization of EST libraries from the porcelain crab, Petrolisthes cinctipes

Jonathon H. Stillman 1 *, Kristen S. Teranishi 2, Abderrhamane Tagmount 3, Erika A. Lindquist 4, and Peter B. Brokstein 4
1 Romberg Tiburon Center, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA; Department of Zoology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
2 Department of Zoology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
3 Romberg Tiburon Center, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA
4 Joint Genome Institute, DOE, 2800 Mitchell Drive, Bldg 400-467, Walnut Creek, CA 94598, USA

* To whom correspondence should be addressed.
Jonathon H. Stillman, E-mail: stillmaj{at}sfsu.edu


  Abstract

Synopsis The thermal phenotype of an organism (heat and cold tolerance, thermal range, and thermal plasticity) is an essential feature of how the organism performs across thermal environments and in response to thermal stress. Porcelain crabs are of interest in addressing questions of thermal phenotype because of their high species diversity and the large variation in thermal phenotype among species, as well as the biogeographic patterning of these crabs along environmental stress gradients. We are studying the cellular bases of thermal phenotype and physiological responses to environmental stress using a functional genomics cDNA microarray approach. To do this, we have isolated total RNA from a range of tissues from 1 species of porcelain crab (Petrolisthes cinctipes) exposed to a suite of thermal conditions, and have used this RNA to construct a 13 824-clone EST library. Here, we describe construction, EST sequencing, assembly and clustering, and results of BLASTx homology search for our initial 13 824-clone library. From 12 060 usable ESTs, 6717 consensus sequences were identified, and roughly 50% of these have homology to known proteins. At present, an additional 50 000-75 000-clone library of P. cinctipes ESTs is being generated, with the aim of developing a library with near-complete coverage of the transcriptome. The libraries and sequence information that will be generated as a result of this project should be of value for crustacean biologists working across a broad range of scientific disciplines (for example, physiology, developmental biology, biological rhythms, ecology, fisheries biology), as well as in studies of molecular evolution and phylogeography.

From the symposium "Genomic and Proteomic Approaches in Crustacean Biology" presented at the annual meeting of the Society for Integrative and Comparative Biology, January 4-8, 2006, at Orlando, Florida.
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