Yazar "Gurcan, Kahraman" seçeneğine göre listele

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    Further investigation of a genetically divergent group of plum pox virus-M strain in Turkey
    (Springer, 2019) Gurcan, Kahraman; Teber, Saffet; Caglayan, Kadriye
    In the past several years, a limited number of isolates of a diverse group of Plum pox virus (PPV) strain -M were discovered in the European part of Istanbul, Turkey. In this study, stone fruit samples were collected from the European part of Istanbul and investigated by PCR typing and sequence analyses for determining prevalence and genetic diversity of this divergent PPV-M isolates. Out of the 230 sampled trees, 97 were determined to be infected with PPV. Strains of 88 isolates were identified and 67 of them (76%) were divergent PPV-M isolates, detected in apricot, peach and plum trees revealing that they could be evolutionarily successful divergent PPV-M isolates prevalent in Istanbul. The divergent Istanbul M isolates formed a monophyletic clade thereby named as PPV-MIs. Additionally, recombination analysis suggested that PPV-MIs isolates could be the donor of the PPV-M-type recombinant fragment of the PPV-Rec strain.
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    Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey
    (Springer, 2021) Gurcan, Kahraman; Teber, Saffet; Akbulut, Mikail; Caglayan, Kadriye
    Plum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position 8450 up to end of genome is considered to come from PPV-M, and the remaining major genomic part is PPV-D-derived. It is regarded as third major PPV strain due to its wide distribution and prevalence in Europe. However, among over a thousand PPV isolates genetically identified in Turkey, only 10 of them (<1%) were characterized as PPV-Rec. The nearly complete genome of eight of the PPV-Rec isolates from European part of Turkey were obtained and analyzed together with PPV-Rec isolates of other countries. All major genomic features were conserved among Turkish PPV-Rec isolates. The genetic diversity of PPV-Rec isolates in Turkey (n = 8, 0.015 +/- 0.001%) was found to be comparable to that observed for the isolates from eight countries (n = 10, 0.014 +/- 0.001%). Particularly, genetic diversity of the minor recombinant fragment for Turkish PPV-Rec isolates was apparently higher (0.016 +/- 0.001%) than the value for the 10 isolates from eight countries (0.011 +/- 0.001%). The high genetic diversity was also demonstrated by high phylogenetic variation in Turkish isolates, indicating a long evolutionary history of PPV-Rec isolates in Turkey. After including Turkish isolates in the recombination analysis, the major putative recombination event of PPV-Rec isolates with a breakpoint around position 8450 was identified again, however the other recently reported putative recombination events were not supported in this study by the algorithms implemented in the RDP software.
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    Molecular and biological characterization of a new mulberry idaeovirus
    (Elsevier, 2021) Gurcan, Kahraman; Turan, Sibel; Teber, Saffet; Kilincer, Ilyas; Uz, Ibrahim; Tamisier, Lucie; Massart, Sebastien
    A virus-like disease with symptoms including mosaic structure, deformation, vein clearing and necrosis on the leaves and deformation, crumbling, and scab on the fruits was detected in black mulberry trees (Morus nigra L.) in Kayseri province of Turkey. A novel positive single-stranded RNA virus with a bipartite genome and the mulberry badnavirus 1 (MBV-1) were detected in the black mulberry trees by high throughput sequencing and bioinformatic analyses. The novel virus RNA1 (5,796/7 nt) encodes a polyprotein (1,808 aa, 204.31 kDa) with three conserved domains, [MTR (aa 294?705), Hel (aa 971?1,226) and RdRp (aa 1,348?1,788)], whereas RNA2 (2,243 nt) encodes two putative proteins, MP (374 aa, 40.98 kDa), and CP (272 aa, 30.59 kDa), separated by an intergenic region of 97 nt. The highest amino acids identities were 70, 57 and 70 % with raspberry bushy dwarf virus (RBDV) for ORF1, MP and CP genes, respectively. The genome organization and phylogenetic analyses suggested that the novel virus is likely a putative new member of the genus Idaeovirus and it has been tentatively named black mulberry idaeovirus (BMIV). Virus survey showed both the BMIV and MBV-1 are likely prevalent in the region. Seven complete (six Turkish and one Iranian) and 41 partial genome sequences of the BMIV isolates revealed moderate genetic diversity (0.033 ? 0.001 %, 0.020 ? 0.002 % and 0.016 ? 0.002 % for RNA1, RNA2, and partial genomes, respectively). Both the BMIV and MBV-1 were detected in all tested pollens (n = 24, 100 %), in seed-borne balck mulberry saplings (n = 96, 100 %).This situation clearly revealed the potential spread risk of both viruses in black mulberry plantations and the necessity of taking precautions.