title: Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus.
abstract: Research investigating the genetic basis of physiological responses has significantly broadened our understanding of the mechanisms underlying organismic response to environmental change. However, genomic data are currently available for few taxa only, thus excluding physiological model species from this approach. In this study we report the transcriptome of the model organism Hyas araneus from Spitsbergen (Arctic). We generated 20,479 transcripts, using the 454 GS FLX sequencing technology in combination with an Illumina HiSeq sequencing approach. Annotation by Blastx revealed 7159 blast hits in the NCBI non-redundant protein database. The comparison between the spider crab H. araneus transcriptome and EST libraries of the European lobster Homarus americanus and the porcelain crab Petrolisthes cinctipes yielded 3229/2581 sequences with a significant hit, respectively. The clustering by the Markov Clustering Algorithm (MCL) revealed a common core of 1710 clusters present in all three species and 5903 unique clusters for H. araneus. The combined sequencing approaches generated transcripts that will greatly expand the limited genomic data available for crustaceans. We introduce the MCL clustering for transcriptome comparisons as a simple approach to estimate similarities between transcriptomic libraries of different size and quality and to analyze homologies within the selected group of species. In particular, we identified a large variety of reverse transcriptase (RT) sequences not only in the H. araneus transcriptome and other decapod crustaceans, but also sea urchin, supporting the hypothesis of a heritable, anti-viral immunity and the proposed viral fragment integration by host-derived RTs in marine invertebrates.
authors.affiliation: Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany. Electronic address: LHarms@gmx.net.
authors.forename: Lars
authors.initials: L
authors.lastname: Harms
authors.forename: Stephan
authors.initials: S
authors.lastname: Frickenhaus
authors.forename: Melanie
authors.initials: M
authors.lastname: Schiffer
authors.forename: Felix C
authors.initials: FC
authors.lastname: Mark
authors.forename: Daniela
authors.initials: D
authors.lastname: Storch
authors.forename: Hans-Otto
authors.initials: HO
authors.lastname: Pörtner
authors.forename: Christoph
authors.initials: C
authors.lastname: Held
authors.forename: Magnus
authors.initials: M
authors.lastname: Lucassen
mesh_terms: D000818:Animals; D000998:Antiviral Agents; D003386:Brachyura / Q000235:genetics*; D033364:Decapoda / Q000235:genetics; D015723:Gene Library; D005880:Gills / Q000737:chemistry; D007109:Immunity / Q000235:genetics; D008297:Male; D008390:Markov Chains; D008121:Nephropidae / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D017385:Sequence Homology; D059467:Transcriptome
chemical_list: D000998:Antiviral Agents; D012194:RNA-Directed DNA Polymerase
keywords: Anti-viral immunity; CEGMA; Core Eukaryotic Genes Mapping Approach; Crustacea; MCL; Markov Clustering Algorithm; Spider crab (Hyas araneus); Transcriptome