Agriculture Reference
In-Depth Information
Jones, 2011). Phylogenetic placement of bio-
logically defined PVY
Z
and PVY
E
isolates was
unknown until 2011, when whole genome se-
quences of PVY
Z
isolate L26 (Kerlan
et al
., 2011)
and PVY
E
isolate Mon (Galvino-Costa
et al
.,
2011) were placed within phylogenetically de-
ined PVY
NTN
and a separate clade between
PVY
N/NA-N
and PVY
NTN
lineages, respectively.
PVY-L26 is a recombinant between “PVY
O
” and
PVY
N
and PVY-Mon between PVY
NTN
and PVY-
NE11 (Hu
et al
., 2009a,b; Galvino-Costa
et al
.,
2011; Kerlan
et al
., 2011). The original PVY
E
type isolate (Kerlan
et al
., 1999; Singh
et al
.,
2008) remains unsequenced. However, when
the CP genes of three original PVY
Z
isolates were
sequenced, they grouped with “PVY
O
” or PVY
N-Wi
(Kehoe and Jones, 2011). Thus, PVY
Z
may fit
into both recombinant and non-recombinant
groupings.
Knowledge that (i) few phylogenetically de-
fined “PVY
O
” isolates have been shown to belong
to biologically defined PVY
O
, (ii) many isolates
are recombinants between “PVY
O
” and PVY
N
,
and (iii) that PVY
Z
may fit within three distinct
phylogenetic groupings which include “PVY
O
”
suggests that use of the name PVY
O
for both re-
sistance and phylogenetic PVY strain groupings
should be reconsidered. Use of PVY
O
as a resist-
ance grouping has historical precedence. Kehoe
and Jones (2011) suggested use of PVY
O
be re-
stricted to isolates defined biologically by their
reactions with gene
Ny
tbr
, and that a letter not
used previously be employed instead (Q), giving
the designation PVY
Q
for the phylogenetic
grouping currently known as “PVY
O
”, and the
designation PVY
N:Q
for the phylogenetic group-
ing PVY
N:O
. Kerlan
et al
. (2011) combined resist-
ance and phylogenetic groupings for PVY
Z
isolate L26, designating it PVY
Z/NTN
. This approach
provides a useful means of avoiding confusion
caused by the different nomenclature systems;
for example, the historical PVY
O
and PVY
Z
iso-
lates sequenced by Kehoe and Jones (2011)
would then become PVY
O/Q
, PVY
Z/Q
, or PVY
Z/N-Wi
.
However, sequence characterization of whole
PVY genomes is still needed with these historical
PVY
Z
isolates.
Singh
et al
. (2008) suggested that newly
found PVY isolates should be described within
the context of the original strain groupings based
on host resistance, and not named using geograph-
ical, cultivar, or place-association designations.
However, within a strain group, amendment of
isolate names using additional codes to show
that the isolate differed at the molecular, sero-
logical, or phenotypic level was acceptable.
They recognized five strain groups based on
host resistance (PVY
C
, PVY
O
, PVY
E
, PVY
Z
,
PVY
N
). They also recognized seven strains based
on a combination of host resistance and whole
genome sequencing (PVY
C
, PVY
O
, PVY
E
, PVY
Z
,
PVY
N
, PVY
NTN
, PVY
N-Wi
/PVY
N:O
). The two recom-
binant strains (PVY
NTN
, PVY
N-Wi
/PVY
N:O
) were
placed within strain group PVY
N
. They also sug-
gested that a more systematic investigation and
characterization of PVY at the biological and
molecular levels should eventually result in a
more meaningful strain concept. Karasev and
Gray (2013a) suggested an increase in the
number of PVY strains to nine (PVY
C
, PVY
O
,
PVY
E
, PVY
Z
, PVY
N
, PVY
N-Wi
, PVY
N:O
, PVY
NA-N
,
PVY-NE11). This change resulted from: (i) treat-
ing the ability to induce veinal necrosis in to-
bacco as a subordinate trait to reactions with
potato cultivar differentials; (ii) including
PVY
NTN
within PVY
Z
; (iii) separating the former
PVY
N-WI
strain into PVY
N-WI
and PVY
N:O
; and (iv)
adding new strains PVY
NA:N
and PVY-NE11.
Treating the ability to induce veinal necrosis in
tobacco as a subordinate trait was because the
viral genetic determinants involved in the in-
duction of veinal necrosis in tobacco were
shown to be distinct from the viral genetic deter-
minants involved in the induction of hypersen-
sitive resistance or PTNRD in potato (e.g. Hu
et al
., 2009b; Galvino-Costa
et al
., 2011; Kerlan
et al
., 2011; Moury
et al
., 2011; Faurez
et al
.,
2012; Tian and Valkonen, 2013). Combining
PVY
NTN
with PVY
Z
was based on findings that
potato differentials reacted similarly to both
(Barker
et al
., 2009; Galvino-Costa
et al
., 2011;
Kerlan
et al
., 2011). Separation of the former
PVY
N-WI
strain into PVY
N-WI
and PVY
N:O
, and
the separate classification of PVY
NA-N
and PVY-
NE11, was because these strains all had mo-
lecular characteristics clearly distinct from
those of other PVY strains (Nie and Singh,
2003a; Lorenzen
et al
., 2006, 2008). An im-
proved multiplex IC-RT-PCR assay was devel-
oped that distinguished these nine PVY strains
(Chikh-Ali
et al
., 2013). However, PVY
N-WI
, PVY
N:O
,
PVY
NA-N
, and PVY−NE11 all still lacked biological
typing data using potato cultivar differen-
tials. As mentioned above, Kehoe and Jones
