Nucleotide sequence alignment and phylogenetic tree analysis of NDV strains.

<p>(a) Nucleotide (nt) sequence alignment of part of the 5′ (downstream) non-translated region (NTR) of the Nucleocapsid protein (N) gene of NDV strains to illustrate the 6-nt insert that is characteristic of 15,192-nt size class viruses. (b) Nt sequence alignment of part of the ORF of the Phosphoprotein (P) gene NDV strains to illustrate the 12-nt insert that is found in many of the 15,198-nt size class viruses. All sequences shown are negative-sense and gaps indicate absence of the insert sequence. The nucleotide residues are color coded; U-violet, A-green, G-yellow and C-blue. (c) Phylogenetic tree analysis based on the nt sequences of complete genomes of NDV strains. Note the clustering of NDV strains with respect to their genome-length. Branches in each cluster is color coded: red-15,186 nt; green-15,192 nt; blue-15,198 nt. The tree was constructed by bootstrap analysis (1000 replications) using the neighbor-joining of the Kimura-2-parameter method for nt differences in the MEGA 4.0 phylogenetic analysis program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103951#pone.0103951-Kumar1" target="_blank">[21]</a>. Scale bar shows number of base substitutions per site. Bootstrap values are shown at the nodes. Note the clustering of unique genome-length viruses. Asterisk (*) indicate the reference for the sequence of strain BC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103951#pone.0103951-Krishnamurthy1" target="_blank">[11]</a>. The genetic class designations are indicated for NDV strains in all three panels.