<i>De novo</i> adult transcriptomes of two European brittle stars: spotlight on opsin-based photoreception

Next generation sequencing (NGS) technology allows to obtain a deeper and more complete view of transcriptomes. For non-model or emerging model marine organisms, NGS technologies offer a great opportunity for rapid access to genetic information. In this study, paired-end Illumina HiSeqTM technology has been employed to analyse transcriptomes from the arm tissues of two European brittle star species, Amphiura filiformis and Ophiopsila aranea. About 48 million Illumina reads were generated and 136,387 total unigenes were predicted from A. filiformis arm tissues. For O. aranea arm tissues, about 47 million reads were generated and 123,324 total unigenes were obtained. Twenty-four percent of the total unigenes from A. filiformis show significant matches with sequences present in reference online databases, whereas, for O. aranea, this percentage amounts to 23%. In both species, around 50% of the predicted annotated unigenes were significantly similar to transcripts from the purple sea urchin, the closest species to date that has undergone complete genome sequencing and annotation. GO, COG and KEGG analyses were performed on predicted brittle star unigenes. We focused our analyses on the phototransduction actors involved in light perception. Firstly, two new echinoderm opsins were identified in O. aranea: one rhabdomeric opsin (homologous to vertebrate melanopsin) and one RGR opsin. The RGR-opsin is supposed to be involved in retinal regeneration while the r-opsin is suspected to play a role in visual-like behaviour. Secondly, potential phototransduction actors were identified in both transcriptomes using the fly (rhabdomeric) and mammal (ciliary) classical phototransduction pathways as references. Finally, the sensitivity of O.aranea to monochromatic light was investigated to complement data available for A. filiformis. The presence of microlens-like structures at the surface of dorsal arm plate of O. aranea could potentially explain phototactic behaviour differences between the two species. The results confirm (i) the ability of these brittle stars to perceive light using opsin-based photoreception, (ii) suggest the co-occurrence of both rhabdomeric and ciliary photoreceptors, and (iii) emphasise the complexity of light perception in this echinoderm class

<i>De novo</i> transcriptome analyses provide insights into opsin-based photoreception in the lanternshark <i>Etmopterus spinax</i>

The velvet belly lanternshark (Etmopterus spinax) is a small deep-sea shark commonly found in the Eastern Atlantic and the Mediterranean Sea. This bioluminescent species is able to emit a blue-green ventral glow used in counter-illumination camouflage, mainly. In this study, paired-end Illumina HiSeqTM technology has been employed to generate transcriptome data from eye and ventral skin tissues of the lanternshark. About 64 and 49 million Illumina reads were generated from skin and eye tissues respectively. The assembly allowed us to predict 119,749 total unigenes including 94,569 for the skin transcriptome and 94,365 for the eye transcriptome while 74,753 were commonly found in both transcriptomes. A taxonomy filtering was applied to extract a reference transcriptome containing 104,390 unigenes among which 38,836 showed significant similarities to known sequences in NCBI non-redundant protein sequences database. Around 58% of the annotated unigenes match with predicted genes from the Elephant shark (Callorhinchus milii) genome. The transcriptome completeness has been evaluated by successfully capturing around 98% of orthologous genes of the « Core eukaryotic gene dataset » within the E. spinax reference transcriptome. We identified potential “light-interacting toolkit” genes including multiple genes related to ocular and extraocular light perception processes such as opsins, phototransduction actors or crystallins. Comparative gene expression analysis reveals eye-specific expression of opsins, ciliary phototransduction actors, crystallins and vertebrate retinoid pathway actors. In particular, mRNAs from a single rhodopsin gene and its potentially associated peropsin were detected in the eye transcriptome, only, confirming a monochromatic vision of the lanternshark. Encephalopsin mRNAs were mainly detected in the ventral skin transcriptome. In parallel, immunolocalization of the encephalopsin within the ventral skin of the shark suggests a functional relation with the photophores, i.e. epidermal light-producing organs. We hypothesize that extraocular photoreception might be involved in the bioluminescence control possibly acting on the shutter opening and/or the photocyte activity itself. The newly generated reference transcriptome provides a valuable resource for further understanding of the shark biology

The presence of lateral photophores correlates with increased speciation in deep-sea bioluminescent sharks

The vast majority of species within the lanternshark genus Etmopterus harbour complex luminescent markings on their flanks, whose functional significance has long remained obscure. Recent studies, however, suggest these enigmatic photophore aggregations to play a role in intraspecific communication. Using visual modelling based on in vivo luminescence measurements from a common lanternshark species, we show that etmopterid flank markings can potentially work as a medium range signal for intraspecific detection/recognition. In addition, using molecular phylogenetic analyses, we demonstrate that the Etmopterus clade exhibits a greater than expected species richness given its age. This is not the case for other bioluminescent shark clades with no (or only few) species with flank markings. Our results therefore suggest that etmopterid flank markings may provide a way for reproductive isolation and hence may have facilitated speciation in the deep-sea

Belgian shipwrecks: hotspots for marine biodiversity

Hard bottom substrates at sea allow the development of communities that are often rich in terms of species diversity. Non-biogenic structures such as shipwrecks are an integral part of these substrates, even if they have an anthropogenic origin and the species assemblages they harbor could be for that reason qualified as 'exotic'. There are 200 recent shipwrecks on the Belgian Continental Shelf (BCS), which represent a large fraction of the hard substrate available locally; their presence has an additional interest if we know that the major part of the English Channel and Southern Bight of the North Sea consists almost exclusively of soft sediments. Five shipwrecks on the BCS will be studied in order to assess the meio- and macrofaunal diversity using direct observations and scuba sampling techniques. The soft sediments close to shipwrecks will also be studied to serve as model for areas relatively undisturbed by fisheries (untrawled). Added to this, the influence of shipwrecks on local hydrodynamics and sediment transport will favor the colonization by fragile epibenthic species and as a consequence increase habitat complexity. For each site, standard abiotic parameters and current vectors will be measured and modeled. The information will be centralized in a database and disseminated through a web site devoted to the biodiversity of the BCS. The results will be relevant to the management of the BCS; the anthropogenic hard substrates of shipwrecks can serve as a model for what will happen with the installation of offshore windmills. A brochure will increase public awareness of the importance of marine diversity, and increase public support for marine protected areas

Belgian shipwreck: hotspots for marine biodiversity BEWREMABI: final report

The main aim of the project is to document the fauna found on five shipwrecks in the Belgian part of the North Sea (map). While we have a fairly good understanding of the fauna of soft bottoms of our part of the North Sea, the fauna of these artificial hard substrates is largely unknown. Study of these habitats will allow us to understand species distribution patterns, and allow us to predict which species to expect on other artificial hard substrates, such as sokkels of wind mills. It is a two year research project carried out in the framework of the SPSD-II research action of the Belgian Federal Science Policy Office

Opsin evolution in the Ambulacraria

Opsins - G-protein coupled receptors involved in photoreception - have been extensively studied in the animal kingdom. The present work provides new insights into opsin-based photoreception and photoreceptor cell evolution with a first analysis of opsin sequence data for a major deuterostome clade, the Ambulacraria. Systematic data analysis, including for the first time hemichordate opsin sequences and an expanded echinoderm dataset, led to a robust opsin phylogeny for this cornerstone superphylum. Multiple genomic and transcriptomic resources were surveyed to cover each class of Hemichordata and Echinodermata. In total, 119 ambulacrarian opsin sequences were found, 22 new sequences in hemichordates and 97 in echinoderms (including 67 new sequences). We framed the ambulacrarian opsin repertoire within eumetazoan diversity by including selected reference opsins from non-ambulacrarians. Our findings corroborate the presence of all major ancestral bilaterian opsin groups in Ambulacraria. Furthermore, we identified two opsin groups specific to echinoderms. In conclusion, a molecular phylogenetic framework for investigating light-perception and photobiological behaviors in marine deuterostomes has been obtained

Early development of bioluminescence suggests camouflage by counter-illumination in the velvet belly lantern shark <i>Etmopterus spinax</i> (Squaloidea: Etmopteridae)

The development of luminous structures and the acquisition of luminescence competence during the ontogeny of the velvet belly lantern shark Etmopterus spinax, a deep-sea squalid species, were investigated. The sequential appearance of nine different luminous zones during shark embryogenesis were established, and a new terminology for them given. These zones form the complex luminous pattern observed in free-swimming animals. The organogenesis of photophores (photogenic organs) from the different luminous zones was followed, and photophore maturation was marked by the appearance of green fluorescent vesicles inside the photocytes (photogenic cells). Peroxide-induced light emissions as well as spontaneous luminescence analysis indicated that the ability of E. spinax to produce light was linked to the presence of these fluorescent vesicles and occured prior to birth. The size of photogenic organs, as well as the percentage of ventral body surface area occupied by the luminous pattern and covered by photophores increased sharply during embryogenesis but remained relatively stable in free-swimming animals. All these results strongly suggest camouflage by counter-illumination in juvenile E. spinax. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isle