Supplementary_Table_3_RNA_viruses.docx

Table S3. List of RNA phage genomes analyzed. CRISPR spacers from all published genomes were tested for similarity to RNA phage genomes listed here

facebook_homenagem_ricadro _27_maio_2015

Confirmation of C. elegans RNA-seq with qRT-PCR. Expression of N2 response genes to Orsay virus infection with RNA-seq was confirmed with qRT-PCR. qRT-PCR results were normalized to cdc-42 before calculating fold-change. (PDF 29 kb

Additional file 2: of An evolutionarily conserved transcriptional response to viral infection in Caenorhabditis nematodes

List of differentially expressed genes upon pathogen infections identified by edgeR. (XLSX 75 kb

Nucleotide alignment identities of AVE001 amplicons from the screening of Rhesus Macaque Study 1.

<p>Top half: pairwise nucleotide identity. Bottom half: number of mismatched nucleotides.</p

Maximum-likelihood phylogenetic analysis of (A) AVE001- and (B) AVE000-positive amplicons.

<p>Red text and asterisks indicate samples from the second time point.</p

Lengths of the coding and untranslated regions of each of the 10 genomic segments of virus XZ0906.

<p>Lengths of the coding and untranslated regions of each of the 10 genomic segments of virus XZ0906.</p

Information of all virus strains used in this study.

<p><b>Note:</b> NA, Not available.</p

Electrophoretic migration patterns of the dsRNA of virus XZ0906 as determined by polyacrylamide gel electrophoresis.

<p>The standard discontinuous polyacrylamide slab gel electrophoresis was used here with a 3.5% acrylamide concentration gel and 10% acrylamide separation gel. After staining with silver nitrate,the genome of XZ0906 was visualized separated into 10 distinct bands.</p

Unique characteristics of novel RNA bacteriophage.

<p>(A) Genome organizations of three novel RNA bacteriophage partial genomes compared to prototypical RNA bacteriophage. (B) EMS013 and (C) Streptomyces bacteriophage ϕ0 genome organizations. ORFs were annotated using protein alignment, conserved domain searching, and structural alignment.</p

Phylogenetic analysis of VP1 amino acid sequences from (A) <i>Reoviridae</i> and (B) <i>Orbivirus</i> strains.

<p>(C) Phylogenetic analysis of T2 amino acid sequences from 29 <i>Orbivirus</i> strains. These analysis employed a neighbor-joining method (using the P-distance algorithm) using the MEGA version 5.04 software package (<a href="http://www.megasoftware.net" target="_blank">www.megasoftware.net</a>). Bootstrap probabilities for each node were calculated using 1000 replicates. Scale bars indicate the number of amino acids substitutions per site. In <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088738#pone-0088738-g005" target="_blank">Figure 5(C)</a>, as many of the available sequences are incomplete, analysis is based on partial sequences (residues 356-567 relative to the BTV-1A sequence). Abbreviations and serotypes (or strain name) are shown in the radial tree image of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088738#pone-0088738-g005" target="_blank">Figure 5</a>. GenBank accession numbers and further details of the sequences can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088738#pone-0088738-t002" target="_blank">Table 2</a>.</p