Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus

Harms, Lars, Frickenhaus, Stephan, Schiffer, Melanie, Mark, Felix C., Storch, Daniela, Pörtner, Hans-Otto, Held, Christoph and Lucassen, Magnus (2013) Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 8 (4). pp. 344-351. DOI 10.1016/j.cbd.2013.09.004.

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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.

Document Type: Article
Keywords: Spider crab (Hyas araneus); Crustacea; Transcriptome; Markov Clustering Algorithm; Anti-viral immunity
Refereed: Yes
Open Access Journal?: No
DOI etc.: 10.1016/j.cbd.2013.09.004
ISSN: 1744-117X
Projects: BIOACID
Date Deposited: 29 Apr 2016 10:37
Last Modified: 29 Apr 2016 10:37
URI: http://oceanrep.geomar.de/id/eprint/32198

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