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. METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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

Response to heat stress in the porcelain crab Petrolisthes cinctipes

Thesis (M.S.)--University of Hawaii at Manoa, 2006.Includes bibliographical references (leaves 62-70).ix, 70 leaves, bound ill. 29 cmThe response to heat stress in the intertidal porcelain crab, Petrolisthes cinctipes, was investigated at the gene expression level. A 13,824 cDNA library was constructed and subsequently used to profile transcriptome changes in crabs during recovery from heat stress. 187 transcripts were either upregulated or downregulated in heat stress versus control groups Ih-30h into recovery from heat stress. Gene expression changes following heat stress involved genes from a wide variety of biological processes, including protein/folding and degradation, cytoskeletal activity, detoxification, energy generation, and lipid metabolism. The majority of expression patterns could be captured by sampling 2h and 18h following heat stress, information important for designing future experiments aiming to determine the effect seasonal changes or latitudinal differences have on the response to heat stress. The present study sets the stage for addressing broader questions relating to how global climate change might affect organisms (i.e. species distribution)