Time series of <i>rbcL</i> sequence composition in <i>Plakobranchus ocellatus</i>.

<p>(A) Relative abundance of respective <i>rbcL</i> in individuals of <i>Plakobranchus ocellatus</i> collected monthly in 2005 and 2007. Source algae of kleptoplasts are shown by abbreviations of the clades (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-t002" target="_blank">Table 2</a>). (B) Tukey's boxplots of the relative abundance of <i>rbcL</i> sequences. Data points of fewer than three individuals of <i>P. ocellatus</i> are shown as diamonds. The brackets with “*” indicate a significant difference of the percentage value in the permuted Brunner-Munzel test. The value beside the symbol “*” indicates p-value.</p

Primer list for sequencing and T-RFLP.

<p> <b>Primers used for PCR and sequencing of mitochondrial 16S rDNA and kleptoplast (chloroplast) </b><b><i>rbcL</i></b><b> genes, and for T-RFLP analysis of </b><b><i>rbcL</i></b><b>.</b></p>*<p> <b>Primers for PCR.</b></p>†<p> <b>Primers for sequencing.</b></p>‡<p> <b>Primer for T-RFLP.</b></p

Phylogenetic tree based on <i>rbcL</i> sequences (continued).

<p>Phylogenetic tree based on <i>rbcL</i> sequences (continued).</p

<i>In silico</i> T-RF lengths of <i>rbcL</i> sequences.

*<p>T-RF lengths of <i>Proposis</i> spp. and <i>Halimeda borneensis</i> were the same and indistinguishable.</p>†<p>T-RF lengths of Halimedineae spp. 1 and Rhipiliaceae spp. were identical and indistinguishable.</p>‡<p><i>Caulerpella</i> spp. was composed of two subtypes having two distinct T-RFs (191 and 291 bp, respectively).</p>§<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-g003" target="_blank">Figures 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-g004" target="_blank">4</a>.</p

δ¹⁵N values of amino acids and estimated trophic positions of <i>Plakobranchus ocellatus</i>, the alga <i>Rhipidosiphon lewmanomontiae</i>, and the giant clam <i>Tridacna crocea</i>.

*<p>Collected off Toguchi, Okinawa, Japan.</p>†<p>Starved for 156 days (5 months) in a laboratory aquarium after collection off Toguchi.</p>‡<p><i>Symbiodinium</i> spp. isolated from the mantle of <i>T. crocea</i>.</p>§<p>‰, relative to air.</p>#<p>Trophic position (TP_Glu/Phe) = (δ¹⁵N_Glu−δ¹⁵N_Phe−3.4)/7.6+1.</p

Phylogenetic tree based on <i>rbcL</i> sequences.

<p>Maximum likelihood (ML) phylogeny of the class Ulvophyceae based on 1254 nucleotide positions of the chloroplast-encoded <i>rbcL</i> gene. The phylogram of the entire tree on the upper left is colored to match the inset. <i>Chlamydomonas reinhardtii</i> (class Chlorophyceae) was chosen as the outgroup. Red, <i>rbcL</i> sequences from <i>P. ocellatus</i>. Black, algal <i>rbcL</i> sequences. Bootstrap support (BS) values >50% are provided at the nodes (neighbor-joining/ML). “-“, BS <50%; “NC”, nonconsensus node that was not observed in the neighbor-joining tree.</p

Number of clones obtained from kleptoplast <i>rbcL</i> clone sequences.

<p>Number of clones obtained in kleptoplast <i>rbcL</i> clone sequencing from each of 7 <i>Plakobranchus ocellatus</i> individuals. The source algae were identified from the phylogenetic analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-g001" target="_blank">Figure 1</a>).</p

Electropherograms of T-RFLP analysis.

<p>T-RFLP electropherograms from (A) <i>Rhipidosiphon lewmanomontiae</i>, (B) <i>Halimeda borneensis</i>, and (C) a single individual of <i>Plakobranchus ocellatus</i> (sample no. Ploc051113A). Fragment lengths and corresponding source algae are shown in the box under the peak. Only a single peak with a length identical to that predicted by <i>in silico</i> T-RFLP was obtained from each algal individual (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-t002" target="_blank">Table 2</a>). The electropherogram from the sea slug (C) showed multiple peaks corresponding to those of <i>in silico</i> T-RFLP of the kleptoplast source algae (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042024#pone-0042024-t002" target="_blank">Table 2</a>).</p

Data Sources

Fasta files with assembled transcriptomes of Carpediemonas-like organism

Protein alignments

Alignments of organellar protein