The statistics of reads used for the miRNA identification.

<p>The statistics of reads used for the miRNA identification.</p

Number of reads present in <i>S</i>. <i>carteri</i> and <i>X</i>. <i>testudinaria</i> that matches known sequences in <i>A</i>. <i>queenslandica</i>.

<p>miRNAs in bold are the mature miRNA, while the unbolded ones are star sequences.</p

List of 11 <i>bona fide</i> miRNAs in <i>S</i>. <i>carteri</i> and 19 in <i>X</i>. <i>testudinaria</i>.

<p>Abbreviations used are ‘aqu’: <i>A</i>. <i>queenslandica</i>; ‘sca’: <i>S</i>. <i>carteri</i>; ‘xte’: <i>X</i>. <i>testudinaria</i>.</p

Maximum-likelihood phylogenies of the core proteins involved in small RNA biogenesis.

<p>Trees were constructed for (A) Argonaute, (B) Piwi, (C) Dicer, (D) Drosha, (E) Pasha, and (F) HEN1. (A), (D), and (F) were constructed using the LG+G amino acid substitution model, while (B), (C), and (E) were constructed using the LG+I+G model. Bootstrap support values are indicated above the branches. Species abbreviations: Ath, <i>Arabidopsis thaliana</i>; Aqu, <i>Amphimedon queenslandica</i>; Cel, <i>Caenorhabditis elegans</i>; Dme, <i>Drosophila melanogaster</i>; Efl, <i>Ephydatia fluviatilis</i>; Hsa, <i>Homo sapiens</i>; Hvu, <i>Hydra vulgaris</i>; Nve, <i>Nematostella vectensis</i>; Sca, <i>S</i>. <i>carteri</i>; Spi, <i>Stylophora pistillata</i>; Spu, <i>Strongylocentrotus purpuratus</i>; and Xte, <i>X</i>. <i>testudinaria</i>. <i>A</i>. <i>thaliana</i> sequences were selected as the outgroup when available. For Piwi, Drosha, and Pasha (whose protein families are not found in plants), sponge sequences were chosen as the outgroup, as they phylogenetically form the most basal clade in the tree.</p

Condition-specific RNA editing in the coral symbiont <i>Symbiodinium microadriaticum</i>

<div><p>RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in 1.6% of all nuclear-encoded genes of <i>Symbiodinium microadriaticum</i>, a dinoflagellate symbiont of reef-building corals. All base-substitution edit types were present, and statistically significant motifs were associated with three edit types. Strikingly, a subset of genes exhibited condition-specific editing patterns in response to different stressors that resulted in significant increases of non-synonymous changes. We posit that this previously unrecognised mechanism extends this organism’s capability to respond to stress beyond what is encoded by the genome. This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts.</p></div

Condition-specific RNA editing in the coral symbiont <i>Symbiodinium microadriaticum</i> - Fig 1

<p><b>Edited sites categorised by (A) 15 most frequently edited genes and (B) editing type.</b> Each bar was further subdivided into equal-width quintiles based on editing frequency. Lighter hues correspond to less frequently edited sites; darker hues to more frequently edited sites. For (B), sites with two or more editing events are lumped together in the "multiple" category.</p

Protein domains of known RNA editing genes and candidate <i>Symbiodinium</i> homologues.

<p>For brevity, one representative sequence was chosen per species for (A) PPR-like and (B) ADAR-like proteins.</p

Distribution of RNA edits in condition-specific and all differentially edited genes.

<p>Intergenic edits are not considered; sites with multiple editing events are considered as separate effects. Category labels are as reported by SnpEff, and p-values were calculated using Fisher’s exact test adjusted for multiple testing (Benjamini-Hochberg).</p

Heatmap of non-synonymous amino acid changes of differentially edited genes.

<p>Original amino acid is on the y-axis, while the post-editing amino acid is on the x-axis. Amino acids are represented as single-letter codes, and coloured according to the property of their side chains: non-polar (red), polar uncharged (blue), acidic (green) and basic (purple).</p

Non-synonymous changes predominate in coding regions of differentially edited genes.

<p>Delta shifts were calculated as the absolute difference of means between stressed and control samples (<i>n</i> ≥ 3 per condition). Shifts in edit frequencies at positions that lead to non-synonymous changes (green) are significantly higher than synonymous ones (blue) for all tested stressors: cold (“16C”), heat (“36C”) and dark (“DS”). <i>p</i>-values were computed from inter-group two-tailed t-tests (*: <i>p</i> < 0.05; **: <i>p</i> < 0.01; ****: <i>p</i> < 0.0001).</p