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    Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N
    (Springer, 2023) Santosa, Adyatma Irawan; Randa-Zelyut, Filiz; Karanfil, Ali; Korkmaz, Savaş; Hartono, Sedyo; Ertunç, Filiz
    Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4–99.0 and 79.1–99.0), P1 (59.1–98.3 and 36.8–98.3), and CP (76.6–100 and 75.7–100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types.
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    Öğe
    Population genetic dynamics of southern tomato virus from Turkey
    (Springer, 2023) Randa-Zelyut, Filiz; Fox, Adrian; Karanfil, Ali
    Southern tomato virus (STV) has been reported from many countries. However, the infection status and population structure of STV in Turkey are unknown. In this study, the presence of STV was investigated in eight provinces across three different geographical regions of Turkey, including the Mediterranean, Aegean, and Marmara regions during the 2019 year vegetation period. Samples from 127 symptomatic and 9 asymptomatic plants from tomato production areas in three different geographical regions of Turkey were tested for a range of tomato infecting viruses using conventional molecular assays. Over 54% of the tomato plants sampled were found to be infected with STV. Also, single, double, and triple infections caused by STV, CMV, a potyvirus, and 16SrXII-A 'Candidatus Phytoplasma Solani' subgroup were detected. The genetic diversity of STV was investigated using the complete coat protein (CP) and RNA-dependent RNA polymerases (RdRp) gene regions of 15 randomly selected STV variants from different geographical regions of Turkey, and global variants accessions from GenBank. Variants from Turkey and other countries showed more than 99% homology with each other. According to the complete CP and RdRp gene regions, phylogenetic analyses revealed two lineages independent of geographical origin and host, and it was observed that all Turkish STV variants clustered in Clade I. Based on the complete CP and RdRP genes of STV, genetic parameters for Turkish and other international variants demonstrated high haplotype diversity and low nucleotide diversity. Negative (purifying) selection, a mechanism that constrains genetic variation, was determined on either CP and RdRp genes of STV. Moreover, based on our best knowledge this study is the first report of STV in Turkey.