Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3′-nontranslated regions

Abstract

Detailed comparisons were made of the sequences of the coat protein (CP) cistrons and 3'-nontranslated regions (3'-NTR) of 21 (geographically) distinct isolates of potato virus Y (PVY) and a virus isolate initially described as pepper mottle virus (PepMoV). Multiple sequence alignments and phylogenetic relationships based on these alignments resulted into a subgrouping of virus isolates which largely corresponded with the historical strain differentiation based on biological criteria as 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 the 3'-terminal region of the potyvirus genome, a distinction could be made between different isolates of one virus species as well as between 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 sequences. This implies a biological significance of these structural elements.

Sequence polymorphism in the 5'NTR and in the P1 coding region of potato virus Y genomic RNA

“…Previous sequence analysis of the capsid protein gene of 21 PVY isolates (among which PVY-Fr and PVY-H are common with our study) indicates a subdivision of the isolates into two groups, in agreement with the historical classification into yo and yN strains based on biological criteria (Van der Vlugt et al, 1993). In contrast, sequence comparison of the 5'NTR (14 isolates) and of the P1 coding region (12 isolates) resulted in a clustering of PVY isolates into three groups.…”

“…Using the 3'NTR as a taxonomic criterion, Van der Vlugt (1993) found that the 'N-type' PVY isolates in his study clustered into the same group. In contrast, the PVY 'N-type' isolates studied in this paper are found either in group I or in group II.…”

“…This indicates a subdivision of isolates inducing 'tobacco veinal necrosis' into two phylogenetically distinct groups. PVY-Fr, which belongs to group II, has been classified by Van der Vlugt et al (1993) in the PVY ° group according to its capsid sequence, and in the PVY N group according to its 3'NTR sequence. Group III contains all the pepper isolates, the Solanum nigrum isolate and two potato isolates, all showing 'O-type' symptoms on tobacco.…”

“…The PVY-Fr isolate has been described as belonging unambiguously to the PVY ~ strain (PVY ring test carried out in Braunschweig, Germany, 1991). However, Van der Vlugt et al (1993) found that it clustered together with PVY ° isolates on the basis of its capsid sequence. The tobacco isolate PVY-NC78 also belongs to group II and causes typical 'tobacco veinal necrosis' symptoms (McDonald & Kristjansson, 1993).…”

Molecular resolution of a complex of potyviruses infecting solanaceous crops at the centre of origin in Peru

“…PVY comprises many strains (De Bokx & Huttinga, 1981;Glais et al, 2002) and those infecting potatoes can be classified into at least four strain groups based on their ability to trigger a hypersensitive resistance response in standard potato cultivars (Jones, 1990;Valkonen et al, 1996). These PVY strain groups are largely consistent with the phylogenetic groups established on the basis of CP-encoding and 39-NTR sequences (Van der Vlugt et al, 1993;Boonham et al, 1999), but there is no experimental data to indicate that either CP or 39-NTR sequences are directly responsible for the symptomatic phenotypes on which the strain group concept is based. Molecular studies on isolates of PVY C indicate that this strain group (or pathotype) consists of two genetic groups (Blanco-Urgoiti et al, 1998), emphasizing that molecular studies increase the resolution of intraspecific variability.…”