2.5 Genome characterization and sequence analysis of thecap, rep genes and PiCV genome
The cap gene sequences, rep gene sequence and the full
genome sequences of PiCV obtained in this study have been deposited in
GenBank, respectively. The sequences obtained in the current study were
compared with all available PiCV sequence data from different
geographical locations within China (n=60) and the rest of the world
(n=73) from the NCBI nucleotide database (Table S1). Multiple sequence
alignments were carried out by ClustalW algorithm using MEGA 5.0
software (Tamura et al., 2011) and the homology among nucleotide and
amino acid sequences was determined by using BioEdit v. 7.0.5 software
(Hall,
1999). A divergence analysis of the Cap protein of PiCV was performed
using WebLogoTm (http://weblogo.threeplusone.com/), an
online software for sequence logo generator (Crooks et al., 2004). A
comparison of entropy (Hx) in amino acid sequences of Cap proteins of
PiCV was carried out by using GraphPad Prism 7.0 software (GraphPad
Software, Inc., USA).