De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean

Lenz, Petra H.; Roncalli, Vittoria; Hassett, R. P.; Wu, Le-Shin; Cieslak, Matthew; Hartline, Daniel K.; Christie, Andrew E.

doi:10.1371/journal.pone.0088589

Cited by 104 publications

(164 citation statements)

References 50 publications

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“…The "DRY" and "NPXXY" motifs, which are highly conserved among G-protein coupled receptors, are indicated by symbols + and $, respectively. crab Limulus polyphemus; Nagata et al, 2010;Eriksson et al, 2013;Battelle et al, 2015) and Crustacea (the Branchiura A. siamensis and the Copedoda Calanus finmarchicus; Sahoo et al, 2013;Lenz et al, 2014) species. Interestingly, EsPeropsin is expressed both in eye and in abdomen.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, we have identified a Peropsin homologue. Peropsin is a non-visual opsin member of Group 4 opsins previously described in vertebrates, Cephalochordata and Artropoda and a retinal-photoisomerase activity has been proposed as its main function (Sun et al, 1997;Koyanagi et al, 2002;Nagata et al, 2010;Eriksson et al, 2013;Battelle et al, 2015, Lenz et al, 2014Henze and Oakley, 2015). Furthermore, using qPCR on RNA isolated from compound eyes, brain and abdomen we detected the tissue expression of the newly identified opsins.…”

Section: Introductionmentioning

confidence: 98%

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The opsin repertoire of the Antarctic krill Euphausia superba

et al. 2016

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The Antarctic krill Euphausia superba experiences almost all marine photic environments throughout its life cycle. Antarctic krill eggs hatch in the aphotic zone up to 1000 m depth and larvae develop on their way to the ocean surface (development ascent) and are exposed to different quality (wavelength) and quantity (irradiance) of light. Adults show a daily vertical migration pattern, moving downward during the day and upward during the night within the top 200 m of the water column. Seawater acts as a potent chromatic filter and animals have evolved different opsin photopigments to perceive photons of specific wavelengths. We have investigated the transcriptome of E. superba and, using a candidate gene approach, we identified six novel opsins. Five are r-type visual opsins: four middle-wavelength-sensitive (EsRh2, EsRh3, EsRh4 and EsRh5) and one long-wavelengthsensitive (EsRh6). Moreover, we have identified a non-visual opsin, the EsPeropsin. All these newly identified opsin genes were significantly expressed in compound eyes and brain, while only EsPeropsin and EsRh2 were clearly detected also in the abdomen. A temporal modulation in the transcription of these novel opsins was found, but statistically significant oscillations were only observed in EsRrh3 and EsPeropsin. Our results contribute to the dissection of the complex photoreception system of E. superba, which enables this species to respond to the daily and seasonal changes in irradiance and spectral composition in the Southern Ocean.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

The opsin repertoire of the Antarctic krill Euphausia superba

et al. 2016

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“…There are Ngaro elements in the crustaceans; these are abundant and expressed in Calanus and Pontastacus (28,29). These elements lack the hydrolase ORF.…”

Section: Ngaro Elements In the Protostomesmentioning

confidence: 99%

Tyrosine Recombinase Retrotransposons and Transposons

Poulter

Butler

2015

Microbiol Spectr

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Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.

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“…Transcriptomic analysis has indicated the presence of multi-copy gene families originating from multiple duplications of an ancestral gene in copepods (Lenz et al 2014;Yang et al 2014), euphausiids (Toullec et al 2013;Sales et al 2017), and pteropods (Maas et al 2015;Thabet et al 2017).…”

Section: Genomic Resources For Marine Zooplanktonmentioning

confidence: 99%

Population Genomics of Marine Zooplankton

Bucklin

DiVito

Smolina

et al. 2018

Population Genomics

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The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many -but not all -marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic "noise" in large and patchy populations from local adaptation to environmental conditions and change.

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De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean

Cited by 104 publications

References 50 publications

The opsin repertoire of the Antarctic krill Euphausia superba

The opsin repertoire of the Antarctic krill Euphausia superba

Tyrosine Recombinase Retrotransposons and Transposons

Population Genomics of Marine Zooplankton

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