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Open Access Research article

Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature

Cristiano De Pittà12, Cristiano Bertolucci3, Gabriella M Mazzotta2, Filippo Bernante1, Giorgia Rizzo2, Barbara De Nardi4, Alberto Pallavicini4, Gerolamo Lanfranchi12 and Rodolfo Costa2*

Author Affiliations

1 CRIBI Biotechnology Centre, Università degli Studi di Padova, Via U. Bassi, 58/B, 35121, Padova, Italy

2 Dipartimento di Biologia, Università degli Studi di Padova, Via U. Bassi, 58/B, 35121, Padova, Italy

3 Dipartimento di Biologia ed Evoluzione, Università degli Studi di Ferrara, Via L. Borsari, 46, 44100 Ferrara, Italy

4 Dipartimento di Biologia, Università degli Studi di Trieste, P.le Valmaura, 9, 34148 Trieste, Italy

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BMC Genomics 2008, 9:45  doi:10.1186/1471-2164-9-45

Published: 28 January 2008

Abstract

Background

Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from different tissues of Euphausia superba (the Antarctic krill).

Results

We have constructed and sequenced five cDNA libraries from different Antarctic krill tissues: head, abdomen, thoracopods and photophores. We have identified 1.770 high-quality ESTs which were assembled into 216 overlapping clusters and 801 singletons resulting in a total of 1.017 non-redundant sequences. Quantitative RT-PCR analysis was performed to quantify and validate the expression levels of ten genes presenting different EST countings in krill tissues. In addition, bioinformatic screening of the non-redundant E. superba sequences identified 69 microsatellite containing ESTs. Clusters, consensuses and related similarity and gene ontology searches were organized in a dedicated E. superba database http://krill.cribi.unipd.it webcite.

Conclusion

We defined the first tissue transcriptional signatures of E. superba based on functional categorization among the examined tissues. The analyses of annotated transcripts showed a higher similarity with genes from insects with respect to Malacostraca possibly as an effect of the limited number of Malacostraca sequences in the public databases. Our catalogue provides for the first time a genomic tool to investigate the biology of the Antarctic krill.