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

Pittà, Cristiano De; Bertolucci, Cristiano; Mazzotta, Gabriella; Bernante, Filippo; Rizzo, Giorgia; Nardi, Barbara De; Pallavicini, Alberto; Lanfranchi, Gerolamo; Costa, Rodolfo

doi:10.1186/1471-2164-9-45

Cited by 24 publications

(26 citation statements)

References 59 publications

(39 reference statements)

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“…Neither can we exclude that other light-input pathways, such as an opsin-based one, could be used for entrainment (Helfrich-Forster et al, 2002). We have previously observed that a novel opsin, which could be involved in the visual signal cascade and in the entrainment of the clock by light cycles of different spectral compositions, is highly expressed in the krill head (De Pittà et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

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ACRYFROM THE KRILL

Mazzotta

Pittà

Benna

et al. 2010

Chronobiology International

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Antarctic krill (Euphausia superba) inhabit a region with strong seasonality in several parameters, such as photoperiod, light intensity, extent of sea ice, and food availability. In particular, seasonal changes in environmental light regimes have been shown to strongly influence krill metabolism, representing control signals for seasonal regulation of physiology of this key Southern Ocean species. Here, we report the identification of a cryptochrome gene, a cardinal component of the clockwork machinery in several organisms. EsCRY appears to be an ortholog of mammalian-like CRYs and clusters with the insect CRY2 subfamily. EsCRY has the canonical bipartite CRY structure, with a conserved N-terminal domain and a highly divergent C-terminus, that bears several binding motifs, some of them shared with insect CRY2 and others peculiar for EsCRY. We have evaluated the temporal expression of Escry both at mRNA and protein levels in individuals harvested from the Ross Sea at different times throughout the 24 h cycle during the Antarctic summer. We observed a daily fluctuation in abundance for Escry mRNA in the head, with high levels around 06:00 h, which is not mirrored by a cycle in the corresponding protein. Our findings represent a first step toward establishing the presence of an endogenous circadian time-keeping mechanism that might allow this organism to synchronize its physiology and behavior to the Antarctic light regimes.

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Section: Discussionmentioning

confidence: 99%

“…Total RNA from dissected organs (head, including brain and compound eyes; abdomen; and thoracopods) was extracted as in De Pittà et al (2008). All the work presented here complies with current regulations covering animal experimentation in Italy and is in accordance with journal standards (Portaluppi et al, 2008).…”

Section: Rna Preparationmentioning

confidence: 99%

ACRYFROM THE KRILL

Mazzotta

Pittà

Benna

et al. 2010

Chronobiology International

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“…While there is considerable scientific knowledge about the krill's biology and ecology, the crustacean's genome sequence is not yet available and a systematic sequencing of cDNA libraries is an efficient approach for the identification of large numbers of transcripts [22], [23]. Clark and colleagues have recently generated the first 454 sequencing data and focused their attention on the typical stress related genes of the Heat Shock Protein family [24].…”

Section: Introductionmentioning

confidence: 99%

The Antarctic Krill Euphausia superba Shows Diurnal Cycles of Transcription under Natural Conditions

et al. 2013

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BackgroundPolar environments are characterized by extreme seasonal changes in day length, light intensity and spectrum, the extent of sea ice during the winter, and food availability. A key species of the Southern Ocean ecosystem, the Antarctic krill (Euphausia superba) has evolved rhythmic physiological and behavioral mechanisms to adapt to daily and seasonal changes. The molecular organization of the clockwork underlying these biological rhythms is, nevertheless, still only partially understood.Methodology/Principal FindingsThe genome sequence of the Antarctic krill is not yet available. A normalized cDNA library was produced and pyrosequenced in the attempt to identify large numbers of transcripts. All available E. superba sequences were then assembled to create the most complete existing oligonucleotide microarray platform with a total of 32,217 probes. Gene expression signatures of specimens collected in the Ross Sea at five different time points over a 24-hour cycle were defined, and 1,308 genes differentially expressed were identified. Of the corresponding transcripts, 609 showed a significant sinusoidal expression pattern; about 40% of these exibithed a 24-hour periodicity while the other 60% was characterized by a shorter (about 12-hour) rhythm. We assigned the differentially expressed genes to functional categories and noticed that those concerning translation, proteolysis, energy and metabolic process, redox regulation, visual transduction and stress response, which are most likely related to daily environmental changes, were significantly enriched. Two transcripts of peroxiredoxin, thought to represent the ancestral timekeeping system that evolved about 2.5 billion years ago, were also identified as were two isoforms of the EsRh1 opsin and two novel arrestin1 sequences involved in the visual transduction cascade.ConclusionsOur work represents the first characterization of the krill diurnal transcriptome under natural conditions and provides a first insight into the genetic regulation of physiological changes, which occur around the clock during an Antarctic summer day.

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“…Starting from 1.5 mg of this RNA, a cDNA library was constructed with a new method recently developed using a combination of the SMART protocol (Clontech), exploiting the templates witching effect at the 5 0 -end and ensuring almost full length cDNA, and Gateway technology (Invitrogen), allowing unidirectional cloning without enzymatic digestion [24]. The D. labrax thymus library was normalized (DlNor) to optimize the discovery rate of the random sequencing process by equilibrating the final representation of abundant and rare transcripts following a protocol previously described [25].…”

Section: Construction Of the Thymus Normalized Cdna Librarymentioning

confidence: 99%

Searching for immunomodulatory sequences in sea bass (Dicentrarchus labrax L.): Transcripts analysis from thymus

Pallavicini

Randelli

Modonut

et al. 2010

Fish & Shellfish Immunology

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The thymus is a key organ of the immune system in most vertebrates and, for this reason, it has been used in this paper for the generation of a normalized cDNA library from sea bass (Dicentrarchus labrax), one of the most extensively cultured species in South Mediterranean aquaculture. A total of 1632 ESTs from this library were initially analysed for sequence quality and vector sequences and, after this control, 1264 (77% of total clones sequenced) high-quality ESTs were further processed. The total collection of D. labrax thymus ESTs has been deposited in the EBI-GenBank-DBJ database (GenBank accession numbers from FN565576 to FN566839). The functional classification of ESTs was performed by Gene Ontology and KEGG annotation and, successively, the sequences were analysed using the ImmunomeBase software to identify potentially immuno-related genes. Using this approach, we found about 100 putative genes involved in immune system responses, most new in sea bass, that were analysed more in detail. Some of the potentially interesting genes identified by these in silico analyses were studied by real-time PCR to verify their expression both at basal level and after in vitro stimulation of sea bass head kidney leukocytes. The used strategy has been confirmed as a good approach to discover new immuno-related genes and to improve the knowledge of specific markers that could help the discrimination of T-cell subpopulations in sea bass and, in general, in Teleosts.

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

Cited by 24 publications

References 59 publications

ACRYFROM THE KRILL

ACRYFROM THE KRILL

The Antarctic Krill Euphausia superba Shows Diurnal Cycles of Transcription under Natural Conditions

Searching for immunomodulatory sequences in sea bass (Dicentrarchus labrax L.): Transcripts analysis from thymus

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