Phylogenetic analysis of picornavirus 3D gene sequences.

<p>Phylogenetic analysis on the basis of amino acid sequence of complete picornavirus 3D gene. The evolutionary history was inferred using the Maximum likelihood method in MEGA5. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) are shown next to the branches. The evolutionary distances were computed using the JTT+G+I method.</p

Prediction of different polyproteins in FHMPV genome.

a<p>7488–7490: Stop codon (TGA).</p

Electron micrograph of fathead minnow picornavirus.

<p>Negative contrast electron microphotograph of FHMPV-03 showing aggregation of non-enveloped spherical (∼ 30–32 nm) virions consistent with virus of the <i>Picornaviridae</i> family. Bar = 200 nm.</p

Phylogenetic analysis of picornavirus complete genome sequences.

<p>Phylogenetic analysis on the basis of complete genome (open reading frame) amino acid sequence of picornavirus. The evolutionary history was inferred using the Maximum likelihood method in MEGA5. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) are shown next to the branches. The evolutionary distances were computed using the JTT+G+I and are in the units of the number of amino acid substitutions per site.</p

Fathead minnow picornavirus infected cell culture.

<p>A) Healthy epithelioma papulosum cyprini cells (EPC), B) EPC cells incubated at 22°C, 6 days post-inoculation with fathead minnow picornavirus (FHMPV-09).</p

Fathead minnow picornavirus genome and diversity.

<p>Sequence divergence of FHMPV with other picornaviruses. A) Sequence identity plot comparing the complete polyprotein of FHMPV-09 and BGPV (YP_006628187.1), green represents amino acid identity between 30%–100% and red represents identity less than 30%. B) Pairwise comparisons of closely related picornaviruses in the P1, P2 and P3 regions. Each number represents the pairwise amino acid identities between the corresponding species.</p

Identification of a VAh-specific genetic region associated with prophage AH4 that is induced after mitomycin C treatment.

<p>(Panel A) Mauve multiple genome alignment of the prophage A4 region from AH strains MN98-04 and AL97-91 with VAh strain ML09-119, depicting the two upstream ORFs (in red) and two within-prophage regions (shown by lack of Mauve alignment) that are VAh-associated. (Panel B) Induced phage DNAs were subjected to 454 pyrosequencing and were reference mapped against the AH4 prophage region of the <i>A. hydrophila</i> Ml09-119 genome. Each predicted ORF is indicated as an arrow, and the four VAH-associated ORFs are depicted in red. </p

Schematic organization of the four different types of O-antigen biosynthesis gene cluster present within the genome of the 11 <i>A. hydrophila</i> isolates sequenced in this study.

<p>All of the genes on the cluster are transcribed in the same direction. All VAh strains along with RAh strain TN97-08 shared the ML09-119-type O-antigen biosynthesis gene cluster. This cluster encodes proteins predicted to be involved in the biosynthesis of the nucleotide sugars D-rhamnose, D-mannose, D-Fucose, and 3-acetamido-3, 6-dideoxy-d-galactose (D-Fuc<i>p</i>3NAc). The AL97-91-type cluster (that was also shared with MN98-04) encodes genes predicted to be required for S-layer biosynthesis and transport in addition to O-antigen biosynthesis. Genes that encode conserved proteins with similar functions are marked with the same color. The number displayed next to the maps indicates the nucleotide positions on the respective contig from each strain. The designation of each of the genes presented on the schematic map of the AL06-01, ML09-119, AL06-06 and AL97-91 O-antigen clusters are found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080943#pone-0080943-t002" target="_blank">Tables 2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080943#pone-0080943-t004" target="_blank">4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080943#pone-0080943-t005" target="_blank">5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080943#pone-0080943-t006" target="_blank">6</a>, respectively.</p

Pan and core-genome plot of 11 different <i>A. hydrophila</i> isolates.

<p>The red and blue lines indicated the number of genes within the core and pan-genomes, respectively. The <i>A. hydrophila</i> core genome contained 3,511 core genes whereas the <i>A. hydrophila</i> pan-genome contained 6,856 genes. Note that the addition of other VAh strains after <i>A. hydrophila</i> ML09-119 did not significantly increase the number of new gene families, which was in agreement with the highly clonal nature of VAh strains. </p

Evolutionary relationships of 37 <i>A. hydrophila</i> taxa based on <i>gyrB</i> gene sequences (out of a larger dataset of 107 <i>A. hydrophila</i><i>gyrB</i> sequences).

<p>The evolutionary history was inferred using the Maximum Parsimony method. Tree #1 out of 67 most parsimonious trees (length = 218) is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths calculated using the average pathway method and are in the units of the number of changes over the whole sequence. </p