Maximum clade credibility tree summarized from the Bayesian molecular clock analysis.

<p>All nodes attained maximal probability support except for those indicated by a * (posterior probability < 0.95). The node age uncertainty is indicated using 95% highest posterior density (HPD) interval bars in blue. Old World and New World ancestral states are indicated by black and red branches/nodes respectively. Nodes of interest are listed A to N as referred in the text.</p

Bayesian phylogeny of the ORF ‘global genus’ amino acid dataset.

<p>Only posterior probabilities of 0.9 are included. The tree is midpoint rooted. Bar, 0.3 substitutions per site.</p

Frameshift stimulatory elements in viruses of the JEV serogroup.

<p>(a) Previously identified frameshift site (Y_CCU_UUU; Y = C or U; orange) and 3'-adjacent stable pseudoknot structure responsible for stimulating-1 PRF in the NS2A-encoding region of JEV and related flaviviruses. Stems 1 and 2 of the pseudoknot are indicated in blue and red respectively. (b) The shift site and pseudoknot are preserved in the newly sequenced KOUV but not in YAOV or CPCV. Substitutions that preserve the base-pairings in stem 1 (blue) or stem 2 (red) of the pseudoknot are indicated in pale blue and orange respectively. In YAOV, a simple stem-loop (brown) was predicted at an appropriate spacing from the shift site to act as a stimulator of-1 PRF. CPCV maintains the shift site but multiple possible 3'-proximal structures (not shown) could be predicted. SLEV sequences lack a suitable shift site at this genomic location. (c) Predicted frameshift stimulatory elements (shift site and 3'-adjacent stem-loop) in YAOV.</p

Bayesian maximum likelihood (ML) phylogenetic tree for CAZV RdRp and related sequences.

<p>The tree is midpoint-rooted and, for clarity, only posterior probability values <u>></u>80% are shown.</p

Codon usage statistics for the RdRp ORFs in the narnavirus-like contigs KF298275 and KF298276.

<p>In-frame forward read-direction stop codons (red) are necessarily absent. Reverse complements of in-frame but reverse read-direction stop codons are highlighted in orange; a single UUA codon corresponds to the UAA stop codon of the >1000-codon reverse-read-direction ORF in KF298276.</p

Common nucleotide polymorphisms observed in AACV and CAZV assemblies.

<p>Only nucleotide variations with a frequency in the mapped reads of at least 20% of the most common nucleotide present at that position are shown. The nucleotide present in the chosen reference assembly is shown first.</p

Neighbour-joining (NJ) phylogenetic tree for the orbivirus-like KF298266 and KF298273 and related sequences.

<p>Nodes with <80% bootstrap support have been collapsed.</p

Analysis of CBPV and AACV sequences.

<p>(A) Map of the CBPV RNA1 genome segment. The region covered by contig KF298264 (AACV) is indicated by the orange bar. The read coverage density is indicated in green. (B) Analysis of variability at synonymous sites in an alignment of the currently available full-length CBPV sequences (EU122229 and EU122231) and AACV (KF298264). Shown are the degree of variability at synonymous sites in a 75-codon sliding window, relative to the average in the ORF1-ORF3 frameshift fusion (obs/exp), and the corresponding statistical significance (<i>p</i>-value). (C) Positions of stop codons in the three forward reading frames in the three sequences (KF298264 - top row of triangles in each panel; CBPV EU122231 and EU122229 - bottom two rows of triangles in each panel). (D, E and F) Corresponding figures for RNA2 (KF298265 - top row of triangles in each panel; CBPV EU122232 and EU122230 - bottom two rows of triangles in each panel). Note that AACV RNA2 lacks a homolog of the CBPV ORF1, and has a shorter 3' UTR than CBPV, as indicated by gaps in the orange bar.</p

Alignments of entomobirnavirus 5' and 3' UTR sequences, indicating that the CAZV sequences are nearly complete.

<p>Initiation and termination codons are highlighted in green and red respectively. Note that both entomobirnavirus segments have upstream AUG codons, although it is not known whether these are utilised. ESV - JN589003/JN589002, CYV - JQ659254/JQ659255, MXV - JX403941/JX403942, CAZV - KF298271/KF298272.</p

Bayesian maximum likelihood (ML) phylogenetic tree for the flavivirus-like KF298267 and related sequences.

<p>The tree is midpoint-rooted and, for clarity, only posterior probability values <u>></u>80% are shown.</p