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


CONCLUSIONS
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.
De Pittà
Cristiano
C
Dipartimento di Biologia, Università degli Studi di Padova, Via U, Bassi, 58/B, 35121, Padova, Italy. cristiano.depitta@unipd.it
Bertolucci
Cristiano
C
Mazzotta
Gabriella M
GM
Bernante
Filippo
F
Rizzo
Giorgia
G
De Nardi
Barbara
B
Pallavicini
Alberto
A
Lanfranchi
Gerolamo
G
Costa
Rodolfo
R
D000818:Animals; D019295:Computational Biology; D033201:Euphausiacea / Q000033:anatomy & histology* / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D018895:Microsatellite Repeats; D009928:Organ Specificity; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic / Q000235:genetics*
D012333:RNA, Messenger