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PLoS One
2016 Jan 01;114:e0152988. doi: 10.1371/journal.pone.0152988.
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De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception.
Delroisse J
,
Mallefet J
,
Flammang P
.
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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.
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Fig 1. Annotation analysis pipeline of the transcriptomes of A. filiformis and O. aranea.
Fig 2. The brittle stars Amphiura filiformis (A-C) and Ophiopsila aranea (D-F). (A) individual in oral view. (B) Feeding arms protruding out of the sediment, in aquarium. (C) Central area of a dorsal arm plate. (D) Individual in aboral view. (E) Feeding arms out of the coralligen, in situ. (F) Central area of a dorsal arm plate showing expanded peripheral trabeculae. (G) Central area of a dorsal arm plate of Ophiocoma wendtii showing microlenses, from [34] (Scale bars: A: 900 μm, B: 1cm, C: 30 μm, D: 5mm, E: 20mm, F: 30 μm, G: 70 μm).
Fig 3. Phototaxis in Ophiopsila aranea.(A-B) Dotplot graph of absolute distance span (A) and speed (B) as calculated from 0 position for each different light conditions. (C-D) Dotplot graph of directional distance span (C) and speed (D) as calculated from 0 position for each different light conditions. Measured distances were taken as positive (+) or negative (−) depending upon whether the brittle star was moving away (+) or toward (-) from the light source. Standard error of the mean is shown for each treatment.
Fig 4. Distributions of contigs and unigenes sizes in Af and Oa transcriptomes.The length of contigs and unigenes ranged from 200 bp to more than 3,000 bp. Each range is defined as follows: sequences within the range of X are longer than X bp but shorter than Y bp.
Fig 5. Distribution of the assembled Af and Oa unigenes in function of the number of reads to which they can be aligned.The x-axis represents the « number of reads » classes.
Fig 6. Distribution of annotation results.Unigenes of Amphiura filiformis and Ophiopsila aranea were annotated using the nr, nt, Swiss-Prot, KEGG, COG and GO databases (see text for details).
Fig 7. (A) E-value distributions, (B) similarity distributions and (C) species distributions of the top BLAST hits for all unigenes from Af and Oa transcriptomes in the nr database.
Fig 8. Gene ontology classification of assembled unigenes from the arm transcriptomes of Amphiura filiformis and Ophiopsila aranea.In both transcriptomes the assignments to the “biological process” category made up the majority of the annotations (Af: 46,641; 47.5%; Oa: 47046, 52.5%) followed by the “cellular component” category (Af: 34,337; 34.9%; Oa: 29,433, 32.9%) and “molecular function” category (Af: 17,280; 17.6%; Oa: 13061, 14.6%). A. The results of the “biological process” category are presented in percentages of the total annotated unigenes. B. The results relative to retinal metabolic process (GO 0042574), retinal binding (GO 0016918), phototransduction (GO 0007602) and visual perception (GO 0007601) are shown.
Fig 9. Deduced amino acid sequences of Ophiopsila aranea opsins (names in bold in the Fig) aligned with closest Strongylocentrotus purpuratus and Amphiura filiformis opsins and Rattus norvegicus rhodopsin.Non-aligned N-terminus and C-terminus ends are cleared up. Transmembrane alpha-helices of Rn rhodopsin are indicated with H. Opsin-specific residues are marked with *. The lysine residue involved in the Schiff base in the position 296 of the R. norvegicus rhodopsin is framed in black. Two cysteine residues potentially involved in a disulfide bond are framed in green (positions equivalent to C110 and C187 in R. norvegicus rhodopsin). A potential palmitoylation motif composed of two contiguous cysteine residues (positions equivalent to C322 and C323 in R. norvegicus rhodopsin) is framed in yellow at the C-terminus. The tyrosine residue (Y) in position equivalent to the glutamate counterion E113 in R. norvegicus rhodopsin, glutamate counterion candidate E181 and DRY-type tripeptide motif (E134/R135/Y136 in R. norvegicus rhodopsin) present at the top of the III TM are framed in blue [85–86]. The pattern “NPxxY(x)6F” (position 302–313 of the R. norvegicus rhodopsin sequence) is framed in purple. Alignment edited in strap software (http://www.bioinformatics.org/strap/) and in SeaView 4.2.12.
Fig 10. Phylogenetic analysis of representative echinoderm opsins, including new Ophiopsila aranea opsins.Sequences cluster into significantly supported subfamilies in Bayesian (illustrated tree) and Maximum Likelihood analyses (see S3 Fig). Branch support values are indicated at important branching points. Branch length scale bar indicates the relative amount of amino acid changes. Sequences are color-coded to indicate their belonging to classical opsin subfamilies (c-opsin in red, r-opsins in blue, neuropsins in pink, Go opsins in green, peropsins in yellow, RGR opsins in orange).
Fig 11. (A) Schematic drawing of canonical phototransduction signalling pathways downstream of r- and c-opsins. (B) Potential molecular actors highlighted in the arm transcriptome of Amphiura filiformis. (C) Potential molecular actors highlighted in the arm transcriptome of Ophiopsila aranea. Actors absent from Af and Oa transcriptome are cleared up. Actors for which a close homologous is present in Af/Oa transcriptome are indicated in blue/red.
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