BLASTx of the 10 most expressed unigenes in the arm transcriptomes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i>.

<p>BLASTx of the 10 most expressed unigenes in the arm transcriptomes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i>.</p

Gene ontology classification of assembled unigenes from the arm transcriptomes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i>.

<p>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.</p

Annotation analysis pipeline of the transcriptomes of <i>A</i>. <i>filiformis</i> and <i>O</i>. <i>aranea</i>.

<p>Annotation analysis pipeline of the transcriptomes of <i>A</i>. <i>filiformis</i> and <i>O</i>. <i>aranea</i>.</p

Distribution of the assembled Af and Oa unigenes in function of the number of reads to which they can be aligned.

<p>The x-axis represents the « number of reads » classes.</p

Phototaxis in <i>Ophiopsila aranea</i>.

<p>(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.</p

Description of the output sequenced data for the adult arm transcriptomes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i>.

<p>Description of the output sequenced data for the adult arm transcriptomes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i>.</p

Deduced amino acid sequences of <i>Ophiopsila aranea</i> opsins (names in bold in the Fig) aligned with closest <i>Strongylocentrotus purpuratus</i> and <i>Amphiura filiformis</i> opsins and <i>Rattus norvegicus</i> rhodopsin.

<p>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 <i>R</i>. <i>norvegicus</i> 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 <i>R</i>. <i>norvegicus</i> rhodopsin). A potential palmitoylation motif composed of two contiguous cysteine residues (positions equivalent to C322 and C323 in <i>R</i>. <i>norvegicus</i> rhodopsin) is framed in yellow at the C-terminus. The tyrosine residue (Y) in position equivalent to the glutamate counterion E113 in <i>R</i>. <i>norvegicus</i> rhodopsin, glutamate counterion candidate E181 and DRY-type tripeptide motif (E134/R135/Y136 in <i>R</i>. <i>norvegicus</i> rhodopsin) present at the top of the III TM are framed in blue [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152988#pone.0152988.ref085" target="_blank">85</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152988#pone.0152988.ref086" target="_blank">86</a>]. The pattern “NPxxY(x)6F” (position 302–313 of the <i>R</i>. <i>norvegicus</i> rhodopsin sequence) is framed in purple. Alignment edited in strap software (<a href="http://www.bioinformatics.org/strap/" target="_blank">http://www.bioinformatics.org/strap/</a>) and in SeaView 4.2.12.</p

Distribution of annotation results.

<p>Unigenes of <i>Amphiura filiformis</i> and <i>Ophiopsila aranea</i> were annotated using the nr, nt, Swiss-Prot, KEGG, COG and GO databases (see text for details).</p

Distributions of contigs and unigenes sizes in Af and Oa transcriptomes.

<p>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.</p

Phylogenetic analysis of representative echinoderm opsins, including new <i>Ophiopsila aranea</i> opsins.

<p>Sequences cluster into significantly supported subfamilies in Bayesian (illustrated tree) and Maximum Likelihood analyses (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152988#pone.0152988.s003" target="_blank">S3 Fig</a>). 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).</p