Raa. Vandervlugt et al., TAXONOMIC RELATIONSHIPS BETWEEN DISTINCT POTATO VIRUS-Y ISOLATES BASED ON DETAILED COMPARISONS OF THE VIRAL COAT PROTEINS AND 3'-NONTRANSLATED REGIONS, Archives of virology, 131(3-4), 1993, pp. 361-375
Detailed comparisons were made of the sequences of the coat protein (C
P) cistrons and 3'-nontranslated regions (3'-NTR) of 21 (geographicall
y) distinct isolates of potato virus Y (PVY) and a virus isolate initi
ally described as pepper mottle virus (PepMoV). Multiple sequence alig
nments and phylogenetic relationships based on these alignments result
ed into a subgrouping of virus isolates which largely corresponded wit
h the historical strain differentiation based on biological criteria a
s host range, symptomatology and serology. Virus isolates belonging to
the same subgroup shared a number of characteristic CP amino acid and
3'-NTR nucleotide residues indicating that, by using sequences from t
he 3'-terminal region of the potyvirus genome, a distinction could be
made between different isolates of one virus species as well as betwee
n different virus species. RNA secondary structure analysis of the 3'-
NTR of twelve PVY isolates revealed four major stem-loop structures of
which, surprisingly, the loop sequences gave a similar clustering of
isolates as resulting from the overall comparisons of CP and 3'-NTR se
quences. This implies a biological significance of these structural el
ements.