عنوان مجله
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ANNALS OF APPLIED BIOLOGY
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کلیدواژهها
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blackberry, coat protein, movement protein, phylogenetic analysis, raspberry, raspberry bushy
dwarf virus, RNA-1, variability
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چکیده
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Raspberry bushy dwarf virus (RBDV), recently renamed to Idaeovirus rubi, is one of
the most common viruses infecting Rubus species worldwide but there is still a
limited number of genome sequences available in the GenBank database and the
majority of the sequences include partial sequences of RNA-1 and RNA-2. The
distribution and incidence of RBDV in main raspberry and blackberry growing provinces in Turkey were monitored during 2015–2019 and 537 Rubus spp. samples were
tested by both DAS-ELISA and RT-PCR. Among the tested samples, 36 samples
tested positive for RBDV by DAS-ELISA and 67 samples by RT-PCR. There was relatively low nucleotide diversity among the Turkish isolates. Turkish isolates shared
93%–97.7%, 84.3%–98.9%, and 85%–99.2% nucleotide sequence identities with
available sequences in the GenBank, in partial RNA-1, movement protein (MP) and
coat protein (CP) genes, respectively. In the phylogenetic tree constructed for
RNA-1, MP, and CP sequences, all Turkish raspberry isolates were clustered in a distinct clade. However, the blackberry isolates showed considerable variation in nucleotide sequences and were placed in three distinct groups. The divergent blackberry
isolates showed high variability in MP (84.5%–89.3%) and CP (85.5%–89.7%) regions
and were placed in a distinct group. The rest of blackberry isolates clustered together
with sweet cherry RBDV isolates adjacent to the grapevine clade or together with
raspberry isolates. The comparative analysis conducted on three RNA segments of
RBDV highlighted the high sequence diversity of Turkish RBDV isolates. This study
also emphasizes the importance of regular monitoring of RBDV infections in Turkey,
with special regard to those Rubus spp. and grapevine accessions employed in conservation and selection programmes. In particular, the presence of new RBDV genetic
variants and infection of Rubus species must be taken into account to choose a correct detection protocol and management strategy.
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