Duplication of tRNA^Sec in hominids.

<p>Pol III binding in human <i>tRNA^Sec1</i> (A) and <i>tRNA^Sec2</i> (B) by Chip-seq (tracks ERR039133 and ERR039141, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#sec016" target="_blank">Materials and Methods</a>). Conserved syntenic genes surrounding <i>tRNA^Sec1</i> (C) and <i>tRNA^Sec2</i> (D) in the genome of five hominids. <i>tRNA^Sec1</i> is flanked by the genes <i>FOSB</i> and <i>RTN2</i>, and <i>tRNA^Sec2</i> is located within an intron of <i>PARVB</i>. (E) Structural alignment of <i>tRNA^Sec1</i> in eleven primates (top) and <i>tRNA^Sec2</i>, only found in hominids (bottom). Panels A and B were produced with the UCSC genome browser [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref060" target="_blank">60</a>] on the human hg19 assembly. “100 Vert. Cons” track corresponds to sequence conservation across 100 vertebrates. Protein coding annotations in panels C and D were obtained with Selenoprofiles [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref024" target="_blank">24</a>]. Sequences in panel E were obtained with Secmarker, aligned using Infernal (cmalign program) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref031" target="_blank">31</a>], and visualized with RALEE [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref061" target="_blank">61</a>]. RALEE highlights the nucleotides that are paired according to the consensus secondary structure at the bottom of the alignment, and that also respect the standard pairing rules. The rightmost column in the alignment corresponds to the discriminator base.</p

Performance statistics of tRNA^Sec prediction for the three programs tested.

<p>Performance statistics of tRNA^Sec prediction for the three programs tested.</p

Structure conservation of tRNA^Sec across eukaryotes.

<p>Arc diagram of eukaryotic tRNA^Sec displaying covariation information. The arcs link the residues that form each pair in the tRNA secondary structure, and are colored according to the covariation (top legend). The blocks correspond to the structural alignment of the tRNA^Sec sequences, and are colored according to the covariation in each sequence (bottom legend). The labels on the right indicate the name of the species, which are clustered by their phylogeny (left panel). Plot produced with R-chie [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref069" target="_blank">69</a>]. In R-chie the covariation values (top legend) have a range of [-2, 2], where -2 is a complete lack of pairing potential and sequence conservation, 0 is complete sequence conservation regardless of pairing potential, and 2 is a complete lack of sequence conservation but maintaining pairing.</p

The discriminator base G73 in tRNA^Sec.

<p>Sequence logos [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref053" target="_blank">53</a>] of the 3’ end of tRNA^Sec candidates from the three domains of life. The subsequences include the AT-stem, starting at position 61 of tRNA (numbering based on [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref035" target="_blank">35</a>]) and extends further into the 3’ region of the gene. The residue in position 73 (the discriminator base) shows a strongly conserved G (guanine). (A) 9/4 fold tRNA cloverleaf structure indicating the 13 base pairs acceptor plus T-arm sequence used in the logos. (B) Bacteria, 2316 sequences; (C) archaea, 20 sequences; (D) eukaryota, 562 sequences; (E) bacterial 7/5 fold tRNA^Sec candidates, including 47 sequences with a shorter 12 bp AT-stem. tRNAs have a poly-T motif in the 3’ region as the transcription termination signal [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref054" target="_blank">54</a>], here only visible in archaea because of the low number of sequences. Only the top scoring candidate in each genome were used to generate the logos.</p

Species with multiple tRNA^Sec candidates.

<p>Species with multiple tRNA^Sec candidates.</p

“Redox-active disulfide protein 2” selenoproteins in <i>Brachyspira</i>.

<p>(A) Multiple sequence alignment containing amino acid sequences obtained from UniRef90 (top four) and from <i>Brachyspira</i> genomes using Selenoprofiles [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref024" target="_blank">24</a>]. In the <i>Brachyspira</i> sequences, the Sec position (column 26) is coloured according to the codon found in the genome: Cys in red; and Sec in green. The thioredoxin domain spans from column 53 to the C-terminus. (B) Genomic arrangement of the three “Redox-active disulfide protein 2” genes, all of them found in a gene cluster in each of the <i>Brachyspira</i> genomes (rows). The genes are coloured according to the codon in the Sec position (marked in black), following the same colouring scheme as panel A. Selenoproteins were either missed or truncated in the annotations provided by NCBI, here represented in darker color and labeled with the NCBI gene name. No annotation was found in NCBI for <i>B. innocent</i> and <i>B. hyodysenteriae</i>. All genes are represented 5’ to 3’; the scale measures nucleotides and is centered on the start codon of the “Sec.1” gene. (C) Structure alignments of the putative SECIS found downstream the TGA codon (underlined in red) in the two selenoproteins, “Sec.1” (left) and “Sec.2” (right). Alignments produced using Infernal [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref031" target="_blank">31</a>] and visualized with RALEE [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref061" target="_blank">61</a>]. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.g006" target="_blank">Fig 6</a> for RALEE colouring scheme.</p

Secondary structure of tRNA^Sec and tRNA^Ser.

<p>Cloverleaf models of tRNA^Sec (A–C) and of a canonical tRNA (tRNA^Ser, D) in <i>Homo sapiens</i> (A and D, eukaryota), <i>Methanococcus maripaludis</i> (B, archaea) and <i>Escherichia coli</i> (C, bacteria). The acceptor arm, D arm, anticodon arm, variable arm and T arm are colored red, yellow, green, blue and purple, respectively. The anticodon triplet UCA (complementary to the UGA codon) is indicated with circled residues. The position 73, known as the discriminator base, is the fourth residue from the 3’ end, and is also circled. tRNA^Sec structures (A–C) were obtained with Secmarker. The tRNA^Ser structure (D) was obtained from tRNAdb 2009 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.ref042" target="_blank">42</a>]. The 3’ terminal CCA triplet is usually encoded in the genome in bacteria, while it is added post-transcriptionally in archaea and eukaryotes. The tRNA^Sec plots are examples of the graphical output of Secmarker.</p

Secmarker web server.

<p>Two snapshots showing the input form (left) and the output page (right). The results shown correspond to the two human tRNA^Sec.</p

tRNA^Sec predictions in archaea genomes.

<p>(A) Phylogenetic tree of the archaeal genomes used in the benchmark set. Sec-containing species are drawn in bold font. Genome names were cut down to species level (not including the strain) for visualization purposes. The complete names including strain identifiers are provided in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.s012" target="_blank">S1 Table</a>. (B) Venn diagram showing the overlap between the tRNA^Sec genes predicted by the three programs. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005383#pcbi.1005383.g002" target="_blank">Fig 2</a> caption for details.</p

RAD tag (SgrAI) derived SNPs from Bombus impatiens

RAD tag (SgrAI) derived SNPs from Bombus impatiens from Sadd et al. (2015) "The genomes of two key bumblebee species with primitive eusocial organisation