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Genetic Diversity in the Coat Protein Genes of Prune dwarf virus Isolates from Sweet Cherry Growing in Turkey.

Öztürk Y, Çevik B - Plant Pathol. J. (2015)

Bottom Line: Sequence comparisons showed 84-99% to 81-100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world.Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups.While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Food Agriculture and Livestock, Eğirdir Fruit Research Station, 32500, Isparta, Turkey.

ABSTRACT
Sweet cherry is an important fruit crop with increasing economical value in Turkey and the world. A number of viruses cause diseases and economical losses in sweet cherry. Prune dwarf virus (PDV), is one of the most common viruses of stone fruits including sweet cherry in the world. In this study, PDV was detected from 316 of 521 sweet cherry samples collected from 142 orchards in 10 districts of Isparta province of Turkey by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). The presence of PDV in ELISA positive samples was confirmed in 37 isolates by reverse transcription- polymerase chain reaction (RT-PCR) method. A genomic region of 862 bp containing the coat protein (CP) gene of PDV was re-amplified from 21 selected isolates by RT-PCR. Amplified DNA fragments of these isolates were purified and sequenced for molecular characterization and determining genetic diversity of PDV. Sequence comparisons showed 84-99% to 81-100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world. Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups. While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed.

No MeSH data available.


Related in: MedlinePlus

The phylogenetic tree showing genetic relationship among PDV cherry isolates from Isparta and different stone fruit production regions the world. The phylogenetic tree was constructed with the CP gene sequences of PDV isolates using Neighbor joining algorithm ClustalX2 and visualized by TreeView program. The CP gene of PRNSV was used as outgroup.
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f4-ppj-31-41: The phylogenetic tree showing genetic relationship among PDV cherry isolates from Isparta and different stone fruit production regions the world. The phylogenetic tree was constructed with the CP gene sequences of PDV isolates using Neighbor joining algorithm ClustalX2 and visualized by TreeView program. The CP gene of PRNSV was used as outgroup.

Mentions: Another phylogenetic analysis was performed only with PDV isolates from sweet cherry To determine genetic relationship and grouping among PDV isolates independent of host variations. When phylogenic analysis was conducted only with PDV isolates from sweet cherry trees, similar phylogenetic grouping was observed. Three major groups were clearly distinguished in phylogenetic tree constructed using nucleotide sequences of only sweet cherry isolates. The largest major group 1 was divided into 2 subgroups (1a and 1b). While major group 2 was also divided in to two smaller sub-groups, group 3 was not divided into subgroups. The majority of PDV isolates from Isparta were placed in major group 1 which was divided into two subgroups. While the subgroup 1a consisted only of Turkish isolates, subgroup contained one isolate from Poland and one isolated from China. The major group 2 consisted of different isolates from diverse geographical origin. Two Turkish PDV isolates, one from Isparta and one from İzmir, were clustered with isolates from five different countries. On the other hand, major group 3 was mostly consisted of Turkish isolates and the cluster contained only two eastern European isolates (Fig. 4). Phylogenetic analyses of nt sequence of the CP gene of PDV isolates only from sweet cherry trees showed no clear association between phylogentic groups and geographic origins of the isolates analyzed. Although the isolates were not grouped according to geographic regions they were collected, some groups consisted mostly from Turkish isolates. The result suggested that lineages of PDV isolates were not developed based on the geographical regions of the isolates but phylogenetic clustering is not completely independent from the geographical origins.


Genetic Diversity in the Coat Protein Genes of Prune dwarf virus Isolates from Sweet Cherry Growing in Turkey.

Öztürk Y, Çevik B - Plant Pathol. J. (2015)

The phylogenetic tree showing genetic relationship among PDV cherry isolates from Isparta and different stone fruit production regions the world. The phylogenetic tree was constructed with the CP gene sequences of PDV isolates using Neighbor joining algorithm ClustalX2 and visualized by TreeView program. The CP gene of PRNSV was used as outgroup.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4356604&req=5

f4-ppj-31-41: The phylogenetic tree showing genetic relationship among PDV cherry isolates from Isparta and different stone fruit production regions the world. The phylogenetic tree was constructed with the CP gene sequences of PDV isolates using Neighbor joining algorithm ClustalX2 and visualized by TreeView program. The CP gene of PRNSV was used as outgroup.
Mentions: Another phylogenetic analysis was performed only with PDV isolates from sweet cherry To determine genetic relationship and grouping among PDV isolates independent of host variations. When phylogenic analysis was conducted only with PDV isolates from sweet cherry trees, similar phylogenetic grouping was observed. Three major groups were clearly distinguished in phylogenetic tree constructed using nucleotide sequences of only sweet cherry isolates. The largest major group 1 was divided into 2 subgroups (1a and 1b). While major group 2 was also divided in to two smaller sub-groups, group 3 was not divided into subgroups. The majority of PDV isolates from Isparta were placed in major group 1 which was divided into two subgroups. While the subgroup 1a consisted only of Turkish isolates, subgroup contained one isolate from Poland and one isolated from China. The major group 2 consisted of different isolates from diverse geographical origin. Two Turkish PDV isolates, one from Isparta and one from İzmir, were clustered with isolates from five different countries. On the other hand, major group 3 was mostly consisted of Turkish isolates and the cluster contained only two eastern European isolates (Fig. 4). Phylogenetic analyses of nt sequence of the CP gene of PDV isolates only from sweet cherry trees showed no clear association between phylogentic groups and geographic origins of the isolates analyzed. Although the isolates were not grouped according to geographic regions they were collected, some groups consisted mostly from Turkish isolates. The result suggested that lineages of PDV isolates were not developed based on the geographical regions of the isolates but phylogenetic clustering is not completely independent from the geographical origins.

Bottom Line: Sequence comparisons showed 84-99% to 81-100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world.Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups.While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Food Agriculture and Livestock, Eğirdir Fruit Research Station, 32500, Isparta, Turkey.

ABSTRACT
Sweet cherry is an important fruit crop with increasing economical value in Turkey and the world. A number of viruses cause diseases and economical losses in sweet cherry. Prune dwarf virus (PDV), is one of the most common viruses of stone fruits including sweet cherry in the world. In this study, PDV was detected from 316 of 521 sweet cherry samples collected from 142 orchards in 10 districts of Isparta province of Turkey by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). The presence of PDV in ELISA positive samples was confirmed in 37 isolates by reverse transcription- polymerase chain reaction (RT-PCR) method. A genomic region of 862 bp containing the coat protein (CP) gene of PDV was re-amplified from 21 selected isolates by RT-PCR. Amplified DNA fragments of these isolates were purified and sequenced for molecular characterization and determining genetic diversity of PDV. Sequence comparisons showed 84-99% to 81-100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world. Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups. While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed.

No MeSH data available.


Related in: MedlinePlus