ena-PROJECT-Alfred Wegener Institute-11-02-2013-10:33:09:164-19
Characterization and analysis of the Arctic spider crab Hyas araneus transcriptome
Background Hyas araneus is a widely distributed crustacean species, which has increasingly become an important organism for pysiological studies investigating the response to environmental changes. Unfortunately, the low availability of genomic data for crustaceans results in a limitation of genomic research investigating the genetic basis of these responses. Results: We could generate 20,479 high quality transcripts, using the 454 GS FLX sequencing technology in combination with an Illumina High Seq sequencing approach. Annotation by BlastX revealed 7,159 blast hits in the NCBI non-redundant (nr) protein database with an E-value cutoff  of 1E-3. The comparison between the H. araneus transcriptome and the EST libraries of Homarus americanus and Petrolisthes cinctipes yielded 3,229/2,581 sequences with a significant hit, using tBlastX with an E-value cutoff of 1E-5. The MCL clustering revealed a common core of 1,186 clusters present in all three species and 5,599 unique clusters for H. araneus. Conclusion: Our study provides the first transcriptome for an Arctic crustacean. The combined sequencing approaches generated high-quality transcripts, that will contribute greatly to the limited genomic data for crustaceans. We introduced the Markov Cluster Algorithm (MCL) clustering for transcriptome comparisons as simple approach to estimate similarities between transcriptomic libraries of different size and quality. Accordingly, our results suggests a high genetic diversity within crustaceans. The present study will be beneficial for future functional genomics on H. araneus and the methodical approach will enhance further transcriptome studies in non-model organisms.
Background Hyas araneus is a widely distributed crustacean species, which has increasingly become an important organism for pysiological studies investigating the response to environmental changes. Unfortunately, the low availability of genomic data for crustaceans results in a limitation of genomic research investigating the genetic basis of these responses. Results: We could generate 20,479 high quality transcripts, using the 454 GS FLX sequencing technology in combination with an Illumina High Seq sequencing approach. Annotation by BlastX revealed 7,159 blast hits in the NCBI non-redundant (nr) protein database with an E-value cutoff  of 1E-3. The comparison between the H. araneus transcriptome and the EST libraries of Homarus americanus and Petrolisthes cinctipes yielded 3,229/2,581 sequences with a significant hit, using tBlastX with an E-value cutoff of 1E-5. The MCL clustering revealed a common core of 1,186 clusters present in all three species and 5,599 unique clusters for H. araneus. Conclusion: Our study provides the first transcriptome for an Arctic crustacean. The combined sequencing approaches generated high-quality transcripts, that will contribute greatly to the limited genomic data for crustaceans. We introduced the Markov Cluster Algorithm (MCL) clustering for transcriptome comparisons as simple approach to estimate similarities between transcriptomic libraries of different size and quality. Accordingly, our results suggests a high genetic diversity within crustaceans. The present study will be beneficial for future functional genomics on H. araneus and the methodical approach will enhance further transcriptome studies in non-model organisms.