Yazar "Ohshima, Kazusato" seçeneğine göre listele

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    First Genome Sequence of Wild Onion Symptomless Virus, a Novel Member of Potyvirus in the Turnip Mosaic Virus Phylogenetic Group
    (Amer Soc Microbiology, 2016) Ohshima, Kazusato; Korkmaz, Savaş; Mitoma, Shinichiro; Nomiyama, Rei; Honda, Yuki
    The nearly complete genome sequence of a new species of potyvirus was obtained from the symptomless wild onion (Allium sp.) in Turkey. This virus has less than 67% nucleotide sequence identities over the polyprotein to other known potyviruses. We propose the name wild onion symptomless virus for this novel potyvirus.
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    Phylogenetic relationships and genetic structure of populations of turnip mosaic virus in Turkey
    (Springer, 2020) Korkmaz, Savaş; Cevik, Bayram; Karanfil, Ali; Onder, Serkan; Ohshima, Kazusato
    Surveys were carried out throughout Turkey and a total of 437 symptomatic samples were collected from winter vegetables and weeds, most of which belong to the Brassicaceae family. Testing the collected samples for the presence of turnip mosaic virus (TuMV) by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) confirmed that 117 samples were infected with TuMV. In total, 20 out of 117 TuMV-infected samples representing different regions and host plants were then selected and further analyzed for biological and molecular characteristics. As a result of biological indexing studies, two host infecting types of TuMV, i.e., B and BR were identified in Turkish TuMV isolates. The partial genomic sequences of the nuclear inclusion b protein and coat protein genes (NIb+CP region) of these isolates were determined. The corresponding sequence of the remaining 61 Turkish TuMV isolates were retrieved from GenBank for further analysis. The phylogenetic analysis showed that Turkish isolates fell into the basal-B, Asian-BR, and world-B phylogenetic groups. The evolutionary divergence value of Turkish isolates in the basal-B, Asian-BR, and world-B phylogroups were determined as 0.0026, 0.0134, and 0.0065 at nucleotide level; 0.0243, 0.0102, and 0.0129 at the amino acid level, respectively. Genetic structure analysis of Turkish TuMV isolates revealed that some isolates were admixed or had migrated among different subgroups. Our analysis provides the first depth study for the biological characteristics and genetic structures of Turkish TuMV populations.
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    Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome
    (Academic Press Inc Elsevier Science, 2016) Ohshima, Kazusato; Matsumoto, Kosuke; Yasaka, Ryosuke; Nishiyama, Mai; Soejima, Kenta; Korkmaz, Savaş; Ho, Simon Y. W.
    Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550-2600 years ago, but that the population mostly radiated 295-545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world. (C) 2015 Elsevier Inc. All rights reserved.