WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

Supplementary material for "WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection", as described in Journal of General Virology. </p

Presumed evolution of the <i>deltaretrovirus</i> pX region.

<p>The deltaretrovirus phylogeny is shown as a cladogram. Conventions are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi-1003162-g003" target="_blank">Figure 3</a>.</p

Layout of a typical training session for patient groups with an autoimmune or autoinflammatory disease.

<p>Layout of a typical training session for patient groups with an autoimmune or autoinflammatory disease.</p

Examples of common questions that trainees and experts would like us to clarify during the training session.

<p>Examples of common questions that trainees and experts would like us to clarify during the training session.</p

Analysis of the codon usage of overlapping frames from the benchmark dataset.

<p>Abbreviations are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi-1003162-t001" target="_blank">Table 1</a>. The last two overlaps have entered their genome by horizontal transfer (see text).</p><p><i>r_sA</i> is the Spearman rank correlation coefficient <i>r_s</i> between the codon usage of the ancestral frame and that of its genome. <i>r_sN</i> is the equivalent coefficient for the <i>de novo</i> frame. N_A and N_N are the number of codons on which <i>r_sA</i> and <i>r_sN</i> were calculated. The first row indicates whether calculations are presented for the actual overlapping frames or for the corresponding simulated frames. The calculation of P for the actual frames is based on Hotelling's t-test, whereas for simulated frames P is based on the distribution of the simulated <i>d₂₁</i> (see text). Agreement between t-Hotelling and simulation is calculated on the basis of whether corresponding P-values are both <0.05 or >0.05.</p

Prediction of the ancestral frame in overlapping genes from the benchmark dataset.

(1)<p>The last two overlaps have entered their genome by horizontal transfer and are not taken into account for calculations of specificity and sensitivity of the method.</p><p>Abbreviations and conventions are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi-1003162-t002" target="_blank">Table 2</a>. A frame is predicted ancestral if its <i>r_s</i> is positive and significantly higher than the <i>r_s</i> of the other frame (P<0.05, corresponding to t-Hotelling >1.70). If no prediction is possible, the field is left blank. Numerical values are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi-1003162-t003" target="_blank">Table 3</a> for actual frames, but are reproduced here for clarity.</p

How we tailor practical workshops for a given disease based on the stage of research.

<p>How we tailor practical workshops for a given disease based on the stage of research.</p

Prediction, by codon usage, of the ancestral frame in overlapping reading frames with identical phylogenetic distribution.

<p>Conventions are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi-1003162-t003" target="_blank">Table 3</a>. A frame is predicted ancestral if its <i>r_s</i> is positive and significantly higher than the <i>r_s</i> of the other frame (P<0.05, corresponding to t-Hotelling>1.70).</p

Benchmark dataset of 27 overlapping genes with known genealogy.

(1)<p>gene overlaps described previously (see reference <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003162#pcbi.1003162-Rancurel1" target="_blank">[3]</a>).</p>(2)<p>additional overlaps collected for this study.</p>(3)<p>The function is that of the overlapping region of the protein; if it is not known, the field is left blank.</p>(4)<p>The NS2 proteins of <i>brevidensoviruses</i> and that of <i>densoviruses</i> are not homologous (they are encoded in different frames relative to NS1).</p>(5)<p>The <i>alphacarmotetravirus</i> polymerase and <i>machlomovirus</i> capsid have originated by horizontal transfer and thus the two corresponding overlaps are not part of the benchmark dataset, although we perform the same analyses on them than on other overlaps(see text).</p><p>Abbreviations: AAP, assembly-activating protein; dsRNA, double-stranded RNA; C-term, C-terminal; L, large envelope protein; MP, movement protein; NABP, nucleic-acid binding protein; NS, non-structural protein; NSs, non-structural protein of the small RNA segment; N-term, N-terminal; Pog, predicted overlapping gene; Pol, Polymerase; SAT, small alternatively translated protein; ssDNA, single-stranded DNA; ssRNA, single-stranded RNA (+, positive or −, negative); TGBp2, Triple Gene Block protein 2; TGBp3, Triple Gene Block protein 3; VP, viral protein.</p

A genomic hotspot of origination of silencing suppressors in plus-strand RNA viruses.

<p>The replicases of <i>Nodaviridae</i> and <i>Bromoviridae</i> contain C-terminal extensions predicted disordered (thin boxes) downstream of their homologous polymerase (RdRP) domain. These extensions encode structurally unrelated suppressors of RNA silencing, B2 and 2b (PDB accession codes respectively 2AZ2 and 2ZI0) in different reading frames. Neither the C-terminal extensions nor the suppressors of RNA silencing have detectable sequence similarity, even between closely related genera. Which region is ancestral in each overlap could not be determined (see text).</p