De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome
| Type | Article | ||||||||||||
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| Date | 2016-08 | ||||||||||||
| Language | English | ||||||||||||
| Author(s) | Harney Ewan1, Dubief Bruno1, Boudry Pierre 2, Basuyaux Olivier3, Schilhabel Markus B.4, Huchette Sylvain5, Paillard Christine1, Nunes Flavia1 |
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| Affiliation(s) | 1 : UEB, Lab Sci Environm Marin LEMAR, Inst Univ Europeen Mer, UMR6539,CNRS,UBO,IRD,Ifremer, Pl Nicolas Copernic, F-29280 Plouzane, France. 2 : UBO, IFREMER, Lab Sci Environm Marin LEMAR, UMR 6539,CNRS,IRD,Ctr Bretagne ZI, F-29280 Plouzane, France. 3 : Ctr Expt, SMEL, F-50560 Blainville Sur Mer, France. 4 : Univ Kiel, Inst Clin Mol Biol, D-24105 Kiel, Germany. 5 : France Haliotis, F-29880 Kerazan Lilia, Plouguemeau, France. |
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| Source | Marine Genomics (1874-7787) (Elsevier Science Bv), 2016-08 , Vol. 28 , P. 11-16 | ||||||||||||
| DOI | 10.1016/j.margen.2016.03.002 | ||||||||||||
| WOS© Times Cited | 31 | ||||||||||||
| Keyword(s) | RNA-Seq, Mollusca, Gastropoda, Development, Vibrio harveyi, Climate change | ||||||||||||
| Abstract | The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata | ||||||||||||
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