Table 1.
Detailed information of the ILTV complete genomes published in GenBank (accessed 2015 November 5) used in the alignment and phylogenetic analyses.
Fig 1.
Representation of the nucleotide and amino acid differences detected in the five ILTV genomes.
The outermost, thick circle is the NCBI ILTV reference sequence (Serva strain, GenBank accession no. HQ630064), where rectangles represent the coding sequences (CDS) and the colour code indicates the transcription strand: cyan refers to CDS in the plus strand, orange stands for minus strand. The inner circles represent the five ILTV genomes sequenced in this study (A = 4787/80, B = 193435/07, C = 757/11, D = MSD CEO vaccine, E = Zoetis CEO vaccine): on each circle, the blue bars indicate silent nucleotide substitutions, while red ones highlight those causing amino acid substitutions. The yellow ribbons in the inner part of the figure connect the coding sequences that are repeated in the ILTV genome. IR: internal repeat; TR: terminal repeat. The plot was obtained with Circos [44].
Table 2.
Results of the pyrosequencing run and genomic assembly (NCBI ILTV Serva reference sequence is reported for comparison).
Table 3.
Pairwise comparison of the five ILTV strains with the NCBI ILTV reference sequence (Serva strain) (global identity percentage and number of identities over the genome length of the shortest of the two).
Table 4.
Summary of nucleotide and amino acid differences in the coding regions of the five ILTV strains vs the genome sequence of the NCBI ILTV reference sequence (Serva strain).
Table 5.
Summary of the amino acid differences in coding regions of the five ILTV strains vs other ILTV complete genomes published in GenBank (accessed 2015 November 5).
Fig 2.
Evolutionary relationships of taxa.
The evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [28] on four different genes: UL27 (A), UL36 (B), ICP4 (C), and sORF4/3 (D). ILTV genomes sequenced in this study are highlighted in red (field strains) and green (vaccine strains). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [45]. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA6 [27].
Fig 3.
Split network showing reticulate evolutionary events of ILTV genomes.
The network was obtained from the nucleotide sequences of Unique Long, Internal Repeat and Unique Short regions of ILTV genome using SplitsTree4 [46] based on the neighbor-net method [47]. The Italian field strains (in red) and the vaccine strains (in green) are closely related to the American CEO vaccines; in the zoomed inset, the split separating the field strains from all the other genomes is highlighted in red, while the one grouping them to the American virulent strain 63140 is in blue.