2.6 Sequence and Phylogenetic analysis
The nucleotide gene sequences of Meq, pp3 and vIL-8 of all MDV strains
were subjected to blast analysis by using NCBI BLAST tool (https:
blast.ncbi.nlm.nih.gov/Blast.cgi) and compared with other MDV strains
available in public domain. A total of 97 sequences including 54 Meq, 25
pp38 and 18 vIL-8 reference gene sequences of MDV of different
pathotypes were retrieved for analysis (supplementary Table 3). The
sequences along with those of the present study were aligned by CLUSTAL
W and annotated using MEGA X version 10.0.5
(www.megasoftware.net) (Kumar et
al., 2018). The best-fit model was selected by comparing the Bayesian
information criterion (BIC) scores. Phylogenetic tree was constructed
separately for each of three genes by using Neighbor-joining method with
1000 bootstrap replicates based on Tamura-Nei model (Tamura and Nei,
1993). All positions containing gaps and missing data were eliminated.