Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors.

Six libraries of expressed sequence tags (ESTs) were constructed by suppression subtractive hybridization (SSH) from the grass shrimp, Palaemonetes pugio, exposed to environmental stress: severe (Dissolved Oxygen (DO) 1.5 mg/L) and moderate (DO 2.5 mg/L) chronic hypoxia, cyclic hypoxia (1.5?7 mg/L), contaminant-induced stress (pyrene and copper), and biological stress (molt). A total of 1553 ESTs were clustered and assembled using Paracel Transcript Assembler software. The resulting 661 potential transcripts included 181 contigs and 480 singlets. The assembled sequences were annotated by BLAST searches against the public protein database. Gene Ontology (GO) terms for each sequence were provided using GOblet software. A total of 312 assembled transcripts matched a protein with an E-value less than 1E-5. The most similar matches (18%) were from different crustaceans. Large proportions of sequences had no significant BLAST hits (53%) or GO terms (64%). GO analysis by libraries showed several genes that were present in only one library suggesting that their expression may be stressor specific. Up-regulation of muscle proteins and GSH-peroxidase appeared specific for chronic (1.5 mg/L) and cyclic hypoxia exposures, respectively. Several genes involved in sulfur redox and (homo)cysteine metabolism were all down-regulated in response to cyclic hypoxia. Up-regulation of cytochrome c oxidase subunit I and down-regulation of vitellogenin was a common response to chronic (1.5 mg/L and 2.5 mg/L) and cyclic DO exposures. The molting process was accompanied by changes in expression of many genes not found in the hypoxia/copper/pyrene libraries. The cDNA clones and sequence information can be used for future functional analysis and for construction of microarrays for monitoring of environmental stressors in coastal waters using wild or caged grass shrimp.