Transcriptome analysis of Crassostrea gigas with short read RNA-Seq

Crassostrea gigasResearchers at the University of Washington used SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes.

To evaluate the effectiveness of restricting characterization solely to short-read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold.

This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.

  • Gavery MR, Roberts SB. (2011) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics [Epub ahead of print]. [abstract]