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Öğe Comprehensive surveillance and population study on plum pox virus in Ankara Province of Turkey(Springer Science and Business Media Deutschland GmbH, 2022) Coşkan, Sevgi; Morca, Ali Ferhan; Akbaş, Birol; Çelik, Ali; Santosa, Adyatma IrawanAnkara Province with its sizeable stone fruits outputs and its geographic location in the middle of Turkey might be one of the diversity centers of plum pox virus (PPV) in the country, yet the epidemiological data from there were rather limited. Multi-year extensive surveillance in all 25 districts of Ankara sampled 8131 Prunus spp. plants to be tested against PPV. DAS-ELISA detected 609 PPV positive samples (7.49%), which were all also confirmed by RT-PCR using two primer pairs to amplify P3-6K1-CI and partial NIb-CP regions. The partial genomes of 80 isolates were sequenced, then the sequences were subjected to phylogenetic and population analyses together with 170 isolates which complete genome sequences available in NCBI GenBank. The phylogenetic study showed that 73 new isolates were PPV-T, six isolates were PPV-M, and one isolate was PPV-D. The subsequent population study confirmed the interesting features of PPV with very high genetic diversities at the species level, thus it should be divided into strains that each retained much lower divergence among isolates. The obtained data also could provide new evidence to separate M, and MIs isolates into two distinct strains. Although previous studies suggested that Turkish isolates have been endemic since a long time ago in the country, the results of demographic analyses of the present study indicated that the expansions of Turkey and Ankara populations were recent, driven by relatively new mutations in their genome. © 2022, The Author(s), under exclusive licence to Deutsche Phytomedizinische Gesellschaft.Öğe First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus(Springer Heidelberg, 2023) Akbaş, Birol; Morca, Ali Ferhan; Çoşkan, Sevgi; Santosa, Adyatma Irawan; Kılıç, Handan Çulal; Çelik, AliThe complete genome of plum pox virus strain T isolates from five different Prunus spp., including almond (P. dulcis) and sour cherry (P. ceracus) isolates, was fully sequenced using the primer pairs designed in this study. The five isolates were aligned with other 50 PPV-T isolates whose complete genome sequences were available in GenBank and then subjected to phylogenetic and diversity analyses. Recombination analysis showed no significant signal detected in the five newly sequenced isolates while confirming four recombinant isolates reported in a previous study. Nucleotide and amino acid phylogenetic trees clustered the tested isolates into three major groups: Balkan 1, 2, and 3. Strain T isolates shared high nucleotide and amino acid identities among them. Diversity analysis applied different parameters to found that the sequences of P3 and 6K1 genes were more conserved over other genes. In accordance, the highly variable P1 and CP genes were found to experience weaker purifying pressures, ? = 0.127 and 0.219, respectively, than other genes. The three neutrality tests gave negative values to all genes, suggesting that strain T populations have expanding or bottleneck selections. Genetic make-up of the only known sour cherry isolate is highly identical to isolates from other Prunus spp. Therefore, this study has updated our knowledge of T strain diversity in new hosts and provided a clear picture of genetic variation and host relationships.Öğe Global population structure of apple mosaic virus (ApMV, Genus Ilarvirus)(MDPI, 2023) Çelik, Ali; Morca, Ali Ferhan; Coşkan, Sevgi; Santosa, Adyatma IrawanThe gene sequence data for apple mosaic virus (ApMV) in NCBI GenBank were analyzed to determine the phylogeny and population structure of the virus at a global level. The phylogenies of the movement protein (MP) and coat protein (CP) genes, encoded by RNA3, were shown to be identical and consisted of three lineages but did not closely correlate with those of P1 and P2, suggesting the presence of recombinant isolates. Recombination Detection Program (RDP v.4.56) detected significant recombination signal in the P1 region of K75R1 (KY883318) and Apple (HE574162) and the P2 region of Apple (HE574163) and CITH GD (MN822138). Observation on several diversity parameters suggested that the isolates in group 3 had higher divergence among them, compared to isolates in groups 1 and 2. The neutrality tests assigned positive values to P1, indicating that only this region experiencing balanced or contracting selection. Comparisons of the three phylogroups demonstrated high Fixation index (F-ST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, & PLUSMN;500 bp of partial MP + 'intergenic region' + partial CP coding regions of two Turkish isolates from apple and seven from hazelnut were sequenced and determined that their phylogenetic positions fell within group 1 and 3, respectively.Öğe Impact of coat protein on evolution of ilarviruses(Academic Press Inc., 2024) Çelik, Ali; Santosa, Adyatma IrawanThe genomic sequences attributed to the coat protein play a pivotal role in the evolutionary trajectory of plant viruses. The coat protein region, particularly scrutinized in the genus of Ilarvirus phylogroups, actively shapes the regional and host-specific dispersion. Within this chapter, assorted insights pertaining to the roles undertaken by coat proteins of frequently encountered Ilarviruses in their evolutionary processes are consolidated. Nonetheless, it is discerned that the availability of genomic data for RNA1 and RNA2 remains markedly limited, impeding the provision of lucid elucidations in this domain. Hence, to comprehensively delineate the evolution of Ilarviruses, a requisite exists for supplementary nucleotide sequence data, with a particular emphasis on taxa that have received lesser attention in research endeavors. © 2024Öğe Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus(MDPI, 2022) Çelik, Ali; Coşkan, Sevgi; Morca, Ali Ferhan; Santosa, Adyatma Irawan; Koolivand, DavoudA total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020–2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ? value range of 0.0869–0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low FST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV. © 2022 by the authors.Öğe Molecular analysis of prune dwarf virus reveals divergence within non-Turkish and Turkish viral populations(Springer, 2023) Santosa, Adyatma Irawan; Çelik, Ali; Glasa, Miroslav; Serçe, Çiğdem Ulubaş; Ertunç, FilizPrune dwarf virus (PDV) infection affects the production of stone fruits (Prunus spp.) around the world, including in Turkey. In this study, we analyzed the available nucleotide (nt) and amino acid (aa) sequences of P1, P2, movement protein (MP), and coat protein (CP) genes to assess the molecular variability and structure of non-Turkish and Turkish PDV populations. Global isolates were clustered into three major groups in nt-based phylogenetic trees of MP and CP. Comparison of geographically different isolates showed that the MP aa sequences were more conserved than the CP aa sequences. The major aa changes in MP and CP showed the most effect on group 3 isolates. MP and CP-based analyses revealed the lowest number of variable sites (S), total number of mutations (eta), average number of nt differences between sequences (k), and nt diversity (per site) (pi) values in group 3 isolates, indicating high genomic similarities. The Turkish isolates manifested the highest S and eta, and the second highest k and pi values were observed in the comparison with CP, confirmed the high intra-group divergence of the Turkish isolates belonging to the three phylogroups. A stronger purifying selection pressure was observed in the MP region than in the CP region. Neutrality tests deduced negative values for all the MP and CP phylogroups and positive values for the P1, P2, Bulgarian, and Polish populations. MP and CP comparisons showed the divergence of the three phylogroups, as revealed by the results of the K-S*, K-ST*, Z*, and S-nn permutation statistical tests. The fixation index (F-ST) values suggested that non-Turkish PDV isolates had a higher genetic distance compared with Turkish isolates from group 3 and the Turkish isolates from the other two groups.Öğe Molecular analysis of the global population of potato virus S redefines its phylogeny, and has crop biosecurity implications(MDPI, 2023) Topkaya, Şerife; Çelik, Ali; Santosa, Adyatma Irawan; Jones, Roger A. C.In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Nigde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP's, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (? = 0.0603-0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.Öğe The monitoring of plum pox virus in Bursa, Bilecik, and Bolu provinces of Turkey refined MIs status as a variant of strain M(Taylor & Francis Ltd, 2022) Çelik, Ali; Santosa, Adyatma Irawan; Ertunç, FilizA total of 486 symptomatic and asymptomatic peach leaf samples were collected from Bursa, Bilecik, and Bolu provinces and tested for plum pox virus (PPV, Potyvirus) in response to recent reports on the new divergent subgroup MIs in the nearby Istanbul province of Turkey. The phylogenetic analysis of newly sequenced isolates indicated that two isolates from Bolu belong to subgroup MIs, confirming the existence of its isolates beyond Istanbul. Both Bolu MIs isolates cross-reacted with a mixture of polyclonal antibodies and monoclonal 5B-IVIA in a commercial DAS-ELISA kit for universal detection of PPV strains, elucidating some of MIs serological characters. The identity percentage, and also the evolutionary distance and diversity analyses showed that M isolates shared high genetic identities among them, and that the diversity among its subgroups was also low. Therefore, the results showed that MIs is not a new distinct strain but a variant of strain M. Supplemental data for this article is available online at https://doi.org/10.1080/03235408.2022.2052523 .Öğe Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey(Academic Press Ltd-Elsevier Science Ltd, 2022) Morca, Ali Ferhan; Çelik, Ali; Coşkan, Sevgi; Santosa, Adyatma Irawan; Akbaş, BirolMolecular identification of tomato spotted wilt virus (TSWV) has been conducted in several surveys in Turkey, but the population structure of the virus in the country remains unknown. During 2019-2020, 227 viral symptomatic tomato (Solanum lycopersicum), pepper (Capsicum annuum), and weeds leaf samples were collected from Ankara, Bartin, Eskisehir, Konya, and Zonguldak provinces. RT-PCR tests confirmed TSWV infection in 99 tomato, pepper, and Chenopodium album samples (43.6%). Phylogenetic analysis based on complete nucleotide sequences of N gene clustered the 23 newly sequenced Turkish isolates and other 281 isolates in NCBI GenBank into three major clades: p202/3WT, Tarquinia, and p105. All tested Turkish isolates were included in either p202/3WT or p105 clade. Global isolates retained high nucleotide and amino acids identity for N gene according to percentage identity analysis. N gene of TSWV was under very strong negative selection pressures, as shown by the very low omega values (<0.15) for all analyzed populations. Three neutrality tests also suggested that these populations are undergoing balancing selection by assigning negative values to most of them. The genetic differentiation and gene flow analysis among three clades demonstrated that they are genetically divergent from each other, but their medium FST values of around 0.5 showed that gene flows among clades are rare. This is the first detailed study on the genetic diversity and population structure of TSWV in Turkey.Öğe Prunus necrotic ringspot virus in Turkey: An immigrant population(Springer Wien, 2022) Çelik, Ali; Santosa, Adyatma Irawan; Gibbs, Adrian J.; Ertunç, FilizAn outbreak in northwestern Turkey of prunus necrotic ringspot virus (PNRSV, genus Ilarvirus, family Bromoviridae) was sampled in 2016-2018. Gene sequences from these isolates, together with all of the gene sequence data for this virus in the GenBank database (>300 non-recombinant coat protein (CP) genes and 20 complete genomic sequences) were analysed to determine the relationship of the Turkish PNRSV isolates to those from other parts of the world. Phylogenetic and population genetic methods independently showed that the most recent common ancestor of the world PNRSV population was probably American, not Eurasian. PNRSV has spread to Turkey on several occasions, as its CP sequences are among the terminal branches of three of the most sampled CP phylogroups. The complete PNRSV genome consists of three segments (RNA1, RNA2, and RNA3), with the larger two encoding replicases and the smallest encoding the movement protein and the CP. One quarter of the RNA1 and RNA2 genes were recombinants. The phylogenies of the CP and MP genes (i.e., different regions of RNA3) were closely correlated but did not correlate with those of RNA1 and RNA2, indicating that some of the isolates were reassortants. However, the non-reassortant ancestor could not be identified, probably because none of the complete genome sequences were from isolates from the basal CP phylogroups. Our results emphasize the importance of strict quarantine, both international and local, for the world's stone fruit crops.Öğe Revealing an Iranian isolate of tomato brown rugose fruit virus: Complete genome analysis and mechanical transmission(MDPI, 2023) Esmaeilzadeh, Fereshteh; Santosa, Adyatma Irawan; Çelik, Ali; Koolivand, DavoudAn analysis of the complete genome sequence of a novel isolate of tomato brown rugose fruit virus (ToBRFV) obtained from tomatoes in Iran and named ToBRFV-Ir is presented in this study. Comprehensive phylogenetic analysis utilizing key viral proteins, including 126 KDa, 183 KDa, movement protein (MP), and coat protein (CP), as well as the complete genome sequence, classified ToBRFV-Ir and 65 isolates from GenBank into three distinct clades. Notably, genetic diversity assessment revealed relatively low variability among the isolates, irrespective of their geographical or clade affiliation. Natural selection analysis based on the complete genome sequence showed that dN/dS values were consistently <1, indicating the prevailing role of negative selection across all populations. Analyses using the Recombination Detection Program and SplitsTree found no evidence of recombination events or signals in the complete genome sequence of the tested isolates. Thus, these results suggest that the genetic composition of ToBRFV remains stable without significant genetic exchange or recombination events occurring. A simple arithmetic comparison of the patristic distances and dates suggested that the time to the most recent common ancestor (TMRCA) of the ToBRFV populations is approximately 0.8 up to 2.7 with the closest tobamoviruses. An evolutionary study of the tested isolates from various countries based on the complete genome suggests Peruvian ancestry. The ToBRF-Ir isolate was successfully transmitted through mechanical inoculations to Solanum lycopersicum and Nicotiana rustica. These findings shed light on the genetic dynamics and transmission mechanisms of ToBRFV, providing valuable insights into its molecular characteristics and potential spread among susceptible plant species.Öğe Turkish isolates of alfalfa mosaic virus belong to a distinct lineage among global population(Academic Press Ltd- Elsevier Science Ltd, 2024) Morca, Ali Ferhan; Akbas, Birol; Santosa, Adyatma Irawan; Topkaya, Serife; Celik, AliComplete RNA3 sequences of 15 alfalfa mosaic virus (AMV) isolates sampled from Afyonkarahisar, Ankara, Konya, Tokat, Kayseri, and Nevs , ehir Provinces of T & uuml;rkiye were obtained using RT-PCR with two primer pairs designed in this study. Molecular and population analyses were performed on them together with 63 global isolates which full genome sequences available in NCBI GenBank. Phylogenetic analysis based on movement protein (MP) and coat protein (CP) regions showed unrelated isolates clustering between the constructed trees, and the new Turkish isolates were dispersed in different phylogroups. Particularly, three new Turkish potato isolates: B6, K1, and K2 occupied a divergent MP lineage, together with one alfalfa isolate from China: ZM1 NX3. S , eta, and k parameters of genetic diversity confirmed that CP were more conserved than MP sequences. The 15 new Turkish isolates shared 95.4 -100% nucleotide and 94 -100% amino acid, and 92.8 -100% nucleotide and 93.3 -100% amino acid identities among themselves at MP and CP regions, respectively. All tested populations were found to be under very strict purifying constraints (dN/dS ratios of 0.061 -0.219), and had undergone recent expansion, probably due to new mutations in their genome, according to diversity and neutrality tests. Fixation index ( F ST ) values obtained by pairwise comparisons of phylogroups were all above 0.33, suggested that the isolates clustering has been done convincingly.
