The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.
BACKGROUND
With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes.


RESULTS
A set of approximately 30K unique sequences (UniSeqs) representing approximately 19K clusters were generated from approximately 98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66% of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.


CONCLUSIONS
The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.
Tagmount
Abderrahmane
A
Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, California, United States of America.
Wang
Mei
M
Lindquist
Erika
E
Tanaka
Yoshihiro
Y
Teranishi
Kristen S
KS
Sunagawa
Shinichi
S
Wong
Mike
M
Stillman
Jonathon H
JH
D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D033364:Decapoda / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data*; D017422:Sequence Analysis, DNA
D018076:DNA, Complementary