Differential gene expression Nanomia bijuga

Next-generation sequencing has become a critical tool for studies of gene expression. In such studies, gene expression is measured by counting how many transcript reads map to each gene in a reference database. Here we use a hybrid sequencing strategy to investigate differential gene expression between functionally specialized polyps and medusae in the siphonophore Nanomia bijuga (Cnidaria). We combine long-read sequencing (Roche 454) to generate the gene reference and short-read sequencing for expression quantification. To examine potential challenges when using a partial gene reference, we collected data with three commercially available short-read expression workflows: Illumina mRNA-seq, SOLiD SAGE, and Helicos DGE.