Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature
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) se...
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ftbiomed:oai:biomedcentral.com:1471-2164-9-45 2023-05-15T13:52:08+02:00 Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature De Pittà, Cristiano Bertolucci, Cristiano Mazzotta, Gabriella M Bernante, Filippo Rizzo, Giorgia De Nardi, Barbara Pallavicini, Alberto Lanfranchi, Gerolamo Costa, Rodolfo 2008-01-28 http://www.biomedcentral.com/1471-2164/9/45 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2164/9/45 Copyright 2008 De Pittà et al; licensee BioMed Central Ltd. Research article 2008 ftbiomed 2008-03-22T00:10:33Z 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 . 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. Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Euphausia superba BioMed Central Antarctic The Antarctic |
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description |
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 . 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. |
format |
Article in Journal/Newspaper |
author |
De Pittà, Cristiano Bertolucci, Cristiano Mazzotta, Gabriella M Bernante, Filippo Rizzo, Giorgia De Nardi, Barbara Pallavicini, Alberto Lanfranchi, Gerolamo Costa, Rodolfo |
spellingShingle |
De Pittà, Cristiano Bertolucci, Cristiano Mazzotta, Gabriella M Bernante, Filippo Rizzo, Giorgia De Nardi, Barbara Pallavicini, Alberto Lanfranchi, Gerolamo Costa, Rodolfo Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
author_facet |
De Pittà, Cristiano Bertolucci, Cristiano Mazzotta, Gabriella M Bernante, Filippo Rizzo, Giorgia De Nardi, Barbara Pallavicini, Alberto Lanfranchi, Gerolamo Costa, Rodolfo |
author_sort |
De Pittà, Cristiano |
title |
Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
title_short |
Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
title_full |
Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
title_fullStr |
Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
title_full_unstemmed |
Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature |
title_sort |
systematic sequencing of mrna from the antarctic krill (euphausia superba) and first tissue specific transcriptional signature |
publisher |
BioMed Central Ltd. |
publishDate |
2008 |
url |
http://www.biomedcentral.com/1471-2164/9/45 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctic Krill Euphausia superba |
genre_facet |
Antarc* Antarctic Antarctic Krill Euphausia superba |
op_relation |
http://www.biomedcentral.com/1471-2164/9/45 |
op_rights |
Copyright 2008 De Pittà et al; licensee BioMed Central Ltd. |
_version_ |
1766256402089639936 |