differential gene expression in the siphonophore nanomia bijuga (cnidaria) assessed with multiple next-generation sequencing workflows差异基因表达的管水母nanomia bijuga(刺细胞动物)评估与多个下一代测序工作流.pdfVIP

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next- Generation Sequencing Workflows 1 2,3 1 1 1 Stefan Siebert *, Mark D. Robinson , Sophia C. Tintori , Freya Goetz , Rebecca R. Helm , Stephen A. 1,4 5 5 1 Smith , Nathan Shaner , Steven H. D. Haddock , Casey W. Dunn * 1 Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America, 2 Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia, 3 Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, 4 Heidelberg Institute for Theoretical Studies, Heidelberg, Germany, 5 Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America Abstract We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular