abdullah güller - Academia.edu (original) (raw)

Papers by abdullah güller

Türk tarım ve doğa bilimleri dergisi, Nov 24, 2023

Cucumber mosaic virus (CMV) and watermelon mosaic virus (WMV) are plant viruses with positive sin... more Cucumber mosaic virus (CMV) and watermelon mosaic virus (WMV) are plant viruses with positive single-stranded RNA genome that infect cucurbits and cause economic losses. Both viruses cause especially mosaic pattern and deformities in leaves, in cucurbit plants. The leaves of 23 melon and 28 watermelon plants showing such symptoms were sampled from different regions of Iğdır province. Samples with and without symptoms were tested by the Reverse Transcription Polymerase Chain Reaction (RT-PCR) using coat protein gene (CP)-specific primers. Polymerization tests amplified DNA fragments of the expected size for CMV and WMV. Some fragments with positive results were purified, bacterial cloned, nucleotide sequences revealed and registered in the GeneBank (NCBI). Sequence analyzes showed that it contained 593 bp and 822 bp for CMV and WMV, corresponding to the partial CP gene. Phylogenetic relationships with isolates from different geographical regions and plant material were investigated for both viruses. The generated phylogenetic tree confirmed that CMV-Iğdır isolate was in Group I and subgroup B, and WMV-Iğdır isolates were in different groups. In addition, coat proteins of virus isolates were characterized by in silico tools. In the current study, the presence WMV of and CMV in watermelon and melon was determined for the first time in Iğdır province, and group/subgroup assignments of CMV were revealed.

Notulae Botanicae Horti Agrobotanici Cluj-napoca, Sep 24, 2023

In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gen... more In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gene regions of the agent, using six novel tomato brown rugose fruit virus (ToBRFV) variants obtained from the production greenhouses in Antalya, where the infection was first detected in Turkey and global variants. Molecular evolutionary analyses using both CP and MP gene regions showed that all variants were distributed in three major clades. Population dynamics studies for both gene regions have shown that there was very low nucleotide diversity and haplotype diversity. The low haplotype diversity for the CP and MP genes indicated almost no recombination status. A strong negative selection was determined for CP and MP gene regions, dN/dS= 0.0877 and dN/dS=0.2104, respectively. Neutrality test results revealed that ToBRFV populations are in an expansion phase. Pairwise comparisons were performed between populations separated in the geographic hierarchy as American, European, and Asian variants, and the findings showed intense gene flow and high genetic similarity (FST<0,33 and migration rate >1). The results of this study reveal the recent population structure of the virus and suggest that necessary precautions should be taken in the international seed trade against contaminated seeds.

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, Dec 31, 2021

Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, Dec 15, 2020

Van ilinde yetiştiriciliği yapılan yonca (Medicago sativa L.) bitkilerinde 2019 yılında virüsleri... more Van ilinde yetiştiriciliği yapılan yonca (Medicago sativa L.) bitkilerinde 2019 yılında virüslerin oluşturduğu simptomlara benzer belirtiler görülmüştür. Gözlenen belirtiler arasında cüceleşme, yapraklarda mozaik deseni ve sararma, rozetlenme ve küçük yaprak oluşumu yer almaktadır. Simptom gösteren ve göstermeyen bitkilerden toplanan 19 yonca yaprak örneğine, virüs genomunu tespit edebilmek için uygun primer çiftleri ile RT-PCR testi uygulanmıştır. Yonca yaprağı örneklerinden şiddetli belirtiye sahip altısı beklenen büyüklükte 700 bp DNA band oluşturmuştur. Bunlar arasından rastgele seçilen ikisi bir plazmid vektörüne klonlanmıştır. Elde edilen rekombinant plazmidler her iki yönde dizilenmiştir. Dizi analizi sonuçlarına göre infekteli yoncalardaki virüsün Yonca mozaik virüs olduğu açığa çıkarılmıştır. Dizi bilgileri MT210179 ve MT210178 erişim numaraları ile gen bankasına yüklenmiştir ve sırasıyla Alakoy Y9 ve Alakoy Y1 olarak isimlendirilmiştir. Her iki dizi için gen bankasına kayıtlı 16 AMV dizisi ile oluşturulan filogenetik ağaca göre, her iki izolat da nükleotit düzeyinde ABD, Brezilya ve Puglia izolatları ile en yüksek benzerlik ve Güney Kore izolatı ile en düşük benzerlik oranı göstermiştir. Ayrıca her iki dizinin birbirleri arasında, 7 nükleotit değişikliği ile %98.45 oranında nükleotit benzerliği gösterdiği ortaya çıkarılmıştır. Gerçekleştirilen litaratür tarama çalışmalarına göre, bu çalışma Türkiye'nin Van ilinde yetiştirilen yonca bitkilerindeki Yonca mozaik virüsü (AMV)' nün ilk raporu ve moleküler analizidir.

Notulae Botanicae Horti Agrobotanici Cluj-Napoca

Seventy-eight tomato and pepper plants showing symptoms were tested for tomato spotted wilt ortho... more Seventy-eight tomato and pepper plants showing symptoms were tested for tomato spotted wilt orthotospovirus (TSWV) using specific primers targeting the full coat protein gene (CP) through RT-PCR. Plant samples were collected in Denizli region, Türkiye during September 2021. The PCR screening results revealed that 23 samples were infected with TSWV, indicating an infection rate of 29.48%. PCR products were subsequently sequenced bidirectionally, and the obtained sequences were deposited in GenBank under the accession numbers ON323583-84 for pepper, and OQ597214 for tomato. Phylogenetic analysis demonstrated a close relationship between the Turkish-Denizli TSWV isolates and previously reported isolates from tomato and pepper plants in Türkiye (KM407603), Hungary (KJ649612), and Serbia (GU369723). Moreover, in this study, three commercial chemicals and five selected phytochemicals were docked against the TSWV CP to assess their binding energies. The docking results indicate that the te...

Turkish Journal of Agriculture and Forestry, 2016

Marigold (Tagetes erecta L.) plants, also called Mexican or Aztec marigold, with symptoms of shoo... more Marigold (Tagetes erecta L.) plants, also called Mexican or Aztec marigold, with symptoms of shoot proliferation, dwarfing, and reddening were observed in ornamental gardens of Van Province (Turkey). Five plants, two of them showing reddening and three symptomless plants, were sampled at the end of September 2014. Genomic DNA isolated from symptomatic and nonsymptomatic plant leaves was used to amplify 16S rDNA fragments by nested polymerase chain reaction (PCR). Of the 5 marigold samples tested by PCR, only the two showing reddening symptoms yielded the expected 1.2-kb DNA fragments. Amplified PCR fragments were cloned into a plasmid vector and transformed into competent Escherichia coli strain JM 109. Recombinant plasmid DNA was isolated and sequenced bidirectionally. The provided sequences were 1244 bp and 1245 bp in length and were designated as isolate 1 and isolate 2, respectively. BLAST analysis of the 16S rDNA sequence and virtual restriction fragment length polymorphism (RFLP) analysis confirmed the presence of the phytoplasma "Candidatus Phytoplasma solani". The in silico virtual RFLP pattern of isolate 1, based on the 16S rDNA F2n/R2 fragment, was identical (similarity coefficient 1.00) to the reference pattern of 16Sr group XII, subgroup A (GenBank accession no.: AF248959). Isolate 1 was identified as a member of 16SrXII-A. Based on the same analyses, isolate 2 showed molecular characteristics different from reference patterns of all previously established 16Sr groups and subgroups. The most similar was the reference pattern of 16Sr group XII, subgroup A (GenBank accession no.: AF248959), with a similarity coefficient of 0.97. This is the first report of naturally occurring "Ca. P. solani" affecting T. erecta, which shows that this plant species is an alternate host of the agent.

Türkiye tarımsal araştırmalar dergisi, Jul 16, 2023

Bean (Phaseolus vulgaris L.) is one of the world's oldest crops with both financial and nutri... more Bean (Phaseolus vulgaris L.) is one of the world's oldest crops with both financial and nutritional importance. Bean common mosaic potyvirus (BCMV) is one of the prevalent viral agents that affect beans across the globe. Determining the presence of the agent in the relevant region is critical for minimizing crop losses by implementing appropriate preventive and control measures. In this study, 73 bean leaf samples were collected from bean-growing areas in the Denizli province of Türkiye in 2022. The samples were screened for the presence of viral agents using Polymerase Chain Reaction (PCR) with specific primers targeting the polypeptide gene. 26 of the bean samples were found to be positive for BCMV. The coat protein gene sequences of two randomly selected positive isolates were sequenced and deposited in the GenBank with accession numbers OQ910196 and OQ910197. The nucleotide sequences of isolates were found to have high similarity with those of isolates identified in various regions of the world. Phylogenetic analysis indicated that these isolates from Denizli, Türkiye were closely related to other Turkish isolates. However, since some Turkish isolates in the cluster associated with the Denizli isolates were identified as belonging to the US-5 or NL-6 strain, the current sequences may be related to these strains. Further research is necessary to identify the exact strain of the Denizli isolates, which could be achieved through the use of a strain differentiation set.

Emirates Journal of Food and Agriculture

A survey of yellow dwarf viruses (YDVs) -associated diseases of wheat plants was performed for th... more A survey of yellow dwarf viruses (YDVs) -associated diseases of wheat plants was performed for the first time in the Şırnak Province, Turkey. In plants wheat cultivated areas, symptoms such as diminished leaf size, dwarfing, yellowing, and reddening of leaves wheat plants were observed in cultivated areas. A total of 441 specimens were collected regardless of showing symptoms and assayed for Barley/Cereal Yellow Dwarf Viruses [B/CYDV] association by PCR tests using virus coat protein gene (CPG)-specific primer pairs. These assays demonstrated that 13.38% (55 samples) were positive to the occurrence of BYDV-PAV (9.73%) and CYDV-RPV (0.73%) for wheat viruses, but no BYDV-MAV, -SGV, and -RMV infections of BYDVs were found in PCR assays of collected samples. In addition, double infection of BYDV-PAV and CYDV-RPV was detected in 12 samples with a 2.91% infection rate. The CPG sequences of randomly selected two isolates were revealed using bacterial cloning and sequencing. Sequences obtai...

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi

Phytoplasmas are dangerous bacteria severely infecting agricultural production worldwide. In the ... more Phytoplasmas are dangerous bacteria severely infecting agricultural production worldwide. In the present study, the identification of phytoplasmas infecting tomato plants showing symptoms such as small leaves, flower abnormalities, stunting, witches' broom, and reddening was performed. Five plants, two symptomatic and three asymptomatic, were tested to verify phytoplasma infection. Total DNA isolated from 5 leaf samples was used as a template for PCR reactions. The phytoplasma agents were confirmed in the two symptomatic samples. BLASTn search of 16S rRNA of two sequences shared identity similarity of 99.84% with ‘Candidatus Phytoplasma australasia’. Computer-simulated virtual RFLP profiles show that the 16S rRNA sequences is identical to the reference pattern of the 16SrII-D subgroup, with a similarity coefficient of 1.00. Based on BLAST, virtual RFLP, and phylogenetic dendrogram, the identified phytoplasma strains are enclosed in the 16SrII-D subgroup. This is the first report...

Journal of the Institute of Science and Technology

Viruses infecting honey bees are diseases that cause infection and economic damage in every devel... more Viruses infecting honey bees are diseases that cause infection and economic damage in every developmental stage of honey bees all over the world. In this study, a survey was conducted to determine the presence and prevalence of two worldwide common honeybee viruses (deformed wing virus [DWV] and chronic bee paralysis virus [CBPV]). 128 apiaries from 9 different localities in the province of Bingöl were visited to determine viral RNA. Collected 384 honey bee samples were tested molecularly (reverse-transcriptase polymerase chain reaction, RTPCR) using genome-specific primers specific to each virus. In molecular tests, 28 of 128 apiaries (21.87%) gave a positive reaction for DWV, but no CBPV pathogen was detected in any apiary. The 711 bp nucleotide sequence revealed by cloning one of the randomly selected positive samples was registered in the gene bank with the accession number MZ357973. According to the BLASTn analysis in the NCBI database, the nucleotide sequence of the DWV agent ...

Ege Üniversitesi Ziraat Fakültesi Dergisi

Objective: The objective of this study was to investigate the group/subgroup of phytoplasma agent... more Objective: The objective of this study was to investigate the group/subgroup of phytoplasma agent in peppers showing phytoplasma symptoms. Material and Methods: In this study, plants collected from Iğdır province in 2020 were analyzed using direct and nested PCR tests, and BLASTn, iphyClassifier, Mega 7, and pDRAW32 programs were used. Results: In the tests performed, approximately 1.2 kb of DNA fragments specific to phytoplasma were obtained. The 16S rRNA nucleotide sequence (1254 bp in length) (OM663745) revealed that it was showed more than 99.44% nucleotide similarity to other ‘Ca. P. trifolii’ members. The tentative RFLP and phylogenetic analyzes performed proved the ‘Ca. P. trifolii’ the infection from the Clover proliferation group (16SrVI) group and subgroup A in symptomatic pepper plants. Conclusion: The presence of ‘Ca. P. trifolii’ in naturally infected peppers in Iğdır province of Turkey was detected using PCR-RFLP and cladistic analysis.

Journal of Apicultural Science

In this study, we conducted a six-month survey to evaluate the current status of three common hon... more In this study, we conducted a six-month survey to evaluate the current status of three common honey bee viruses (black queen cell virus [BQCV], acute bee paralysis virus [ABPV], and sacbrood virus [SBV]) in Turkey’s Bingöl region and revealed their phylogenetic relationships with the same types of viruses in other parts of the world. We randomly sampled 384 worker honey bees from a total of 128 apiaries from different locations of this region. Molecular tests confirmed the presence of SBV and BQCV, with infection rates of 7.03% and 11.7%, respectively, but ABPV could not be detected in any of the surveyed apiaries. In addition, double infection was detected in an apiary with an infection rate of 0.78%. The sequences of a partial polyprotein gene region of a randomly selected isolate from each detected virus were collected and registered in GenBank under the accession numbers MZ357971 and MZ357972 for SBV and MZ357974 for BQCV. The nucleotide sequence similarity of Turkish BQCV and S...

Turkish Journal of Agricultural and Natural Science, Dec 16, 2021

European Journal of Science and Technology, 2022

Kabak (Cucurbita pepo L.), Türkiye'nin tüm coğrafi bölgelerinde yetiştirilen önemli bir üründ... more Kabak (Cucurbita pepo L.), Türkiye'nin tüm coğrafi bölgelerinde yetiştirilen önemli bir üründür. Zucchini yellow mosaic virus (ZYMV), kabakgiller (Cucur-bitaceae) familyasının tüm türlerini etkilemekte ve yıkıcı etkisinden dolayı bü-yük ekonomik zararlara neden olmaktadır. Kabak türleri ve genotipleri, ZYMV'ne dayanıklılık için uzun süredir dünyanın birçok bölgesinde taranmak-tadır. Literatürde ZYMV'ye dayanıklı genetik kaynaklar rapor edilmiş olsa da, gerçekte bu kaynakların virüsün kimi şiddetli ırklarına karşı dayanıksız oldukları bildirilmektedir. Bu nedenle yürütülen bu çalışma ile ZYMV'ye dayanıklılık gösteren kabak çeşitlerinin veya genotiplerinin sayısının arttırılması hedeflen-miştir. Çalışmada 2005 yılında Kırşehir, Kayseri, Sakarya, Tekirdağ, Nevşehir ve Konya'dan toplanan genotipler kullanılmıştır. 2006 ve 2010 yılları arasında bu genotiplerin kedilenmesi ve seleksiyonu gerçekleştirilmiş ve S5 generasyon-ları üretilmiştir. Yüksek verimli, albenisi yük...

European Journal of Science and Technology, 2022

Ribosome-inactivating proteins (RIPs) are one of the enzymes that inhibit protein synthesis after... more Ribosome-inactivating proteins (RIPs) are one of the enzymes that inhibit protein synthesis after depurination of a specific adenine in ribosomal RNA. The tritin is one of type I RIPs that include RNA-N glycosidase domain from RIP family. In the present study, cDNA encoding tritin from leaves of wheat Kutluk-94 cultivar was isolated and cloned into pGEM-T Easy vector. The recombinant plasmid was sequenced. The different bioinformatics tools were used for assessment of tritin protein characteristics. A total of 38 tritin-like sequences were identified in some monocot plants. Results showed that tritin protein have conserved domain (Ricin-A) found in other RIPs associated with RNA N-glycosidase activity and shows chancing homology to the RIPs in other plant species. According to multiple sequence alignment, tritin has conserved amino acids which are crucial role in RNA N-glycosidase activity. Our study illustrates that results obtained from in silico analyses could provide a perspective to another researcher about molecular and structural properties of tritin protein.

Plant Protection Science, 2021

Phytoplasma-like symptoms of leaf yellowing and calyx malformation were observed in eggplant (Sol... more Phytoplasma-like symptoms of leaf yellowing and calyx malformation were observed in eggplant (Solanum melongena L.), upward leaves and fruit malformation in pepper (Capsicum annuum L.), and aerial tuber formation in potato (S. tuberosum L.) during the survey performed in the late season (August to September) of 2015 and 2016 in Van province (Turkey). A total of 100 samples were tested by nested-PCR using universal primer pairs to assess the sanitary status of the solanaceous crops and to characterise the phytoplasma isolates. Among them, seven samples resulted in a 1.25 kb DNA fragment, and five (two eggplants, two peppers, and one potato) were molecularly characterised (Accession No.: KY579357, KT595210, MF564267, MF564266, and MH683601). BLAST and the virtual restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes revealed the presence of two distinct phytoplasma infections in solanaceous crops: ‘Candidatus Phytoplasma trifolii’ a member of the clover proliferat...

ISPEC Journal of Agricultural Sciences, 2021

Fusarium spp is one of the major phytopathogenic microfungus strains causing severe losses in man... more Fusarium spp is one of the major phytopathogenic microfungus strains causing severe losses in many economically cultivated crops. The soil-borne pathogen Fusarium solani has historically been considered a serious agent across the globe, causing vascular wilt and root rot in agroeconomic crops and eventually leading to plant death. Three different concentrations (1 µl, 2 µl, and 4 µl) of essential oils (EO) extracted from lavender (Lavandula officinalis L.) and summer savory (Satureja hortensis L.) plants were mixed separately with PDA medium, and their antifungal effect against F. solani was investigated in vitro. When the results of the experiment were evaluated statistically, it was determined that the increasing concentrations of summer savory essential oil repressed the mycelial growth of the fungus, while lavender oil did not have any positive or negative effects. The inhibition activity of summer savory EO on F. solani was calculated as 43, 53, and 90% at the concentrations of...

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 2021

Tomato plants displaying severe fruit deformation, flower sterility, aerial rooting, purplish lea... more Tomato plants displaying severe fruit deformation, flower sterility, aerial rooting, purplish leaves and leaf rolling were observed in tomato fields at Van province (Turkey). Samples were collected and total DNA was extracted from symptomatic and asymptomatic plants. Nested polymerase chain reaction (nested-PCR) assays were performed to amplify 16S rDNA sequences for molecular detection using universal primer pairs. Out of 100 tested tomato samples, 11% of tomato samples yielded a DNA fragment of 1.25 kb. Amplified PCR products were then cloned into pGEM T-Easy vector and sequenced using new generation DNA sequencing (NGS) system. The virtual restriction fragment length polymorphism (RFLP) analysis of 16S rDNA sequences and molecular detections were allowed to characterize possible phytoplasmas associated with diseased plants. Our results revealed the presence of two phytoplasma species belonging to two different ribosomal groups; ‘Candidatus Phytoplasma trifolii’ (16Sr VI-A group) ...

Türk tarım ve doğa bilimleri dergisi, Nov 24, 2023

Cucumber mosaic virus (CMV) and watermelon mosaic virus (WMV) are plant viruses with positive sin... more Cucumber mosaic virus (CMV) and watermelon mosaic virus (WMV) are plant viruses with positive single-stranded RNA genome that infect cucurbits and cause economic losses. Both viruses cause especially mosaic pattern and deformities in leaves, in cucurbit plants. The leaves of 23 melon and 28 watermelon plants showing such symptoms were sampled from different regions of Iğdır province. Samples with and without symptoms were tested by the Reverse Transcription Polymerase Chain Reaction (RT-PCR) using coat protein gene (CP)-specific primers. Polymerization tests amplified DNA fragments of the expected size for CMV and WMV. Some fragments with positive results were purified, bacterial cloned, nucleotide sequences revealed and registered in the GeneBank (NCBI). Sequence analyzes showed that it contained 593 bp and 822 bp for CMV and WMV, corresponding to the partial CP gene. Phylogenetic relationships with isolates from different geographical regions and plant material were investigated for both viruses. The generated phylogenetic tree confirmed that CMV-Iğdır isolate was in Group I and subgroup B, and WMV-Iğdır isolates were in different groups. In addition, coat proteins of virus isolates were characterized by in silico tools. In the current study, the presence WMV of and CMV in watermelon and melon was determined for the first time in Iğdır province, and group/subgroup assignments of CMV were revealed.

Notulae Botanicae Horti Agrobotanici Cluj-napoca, Sep 24, 2023

In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gen... more In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gene regions of the agent, using six novel tomato brown rugose fruit virus (ToBRFV) variants obtained from the production greenhouses in Antalya, where the infection was first detected in Turkey and global variants. Molecular evolutionary analyses using both CP and MP gene regions showed that all variants were distributed in three major clades. Population dynamics studies for both gene regions have shown that there was very low nucleotide diversity and haplotype diversity. The low haplotype diversity for the CP and MP genes indicated almost no recombination status. A strong negative selection was determined for CP and MP gene regions, dN/dS= 0.0877 and dN/dS=0.2104, respectively. Neutrality test results revealed that ToBRFV populations are in an expansion phase. Pairwise comparisons were performed between populations separated in the geographic hierarchy as American, European, and Asian variants, and the findings showed intense gene flow and high genetic similarity (FST<0,33 and migration rate >1). The results of this study reveal the recent population structure of the virus and suggest that necessary precautions should be taken in the international seed trade against contaminated seeds.

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, Dec 31, 2021

Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, Dec 15, 2020

Van ilinde yetiştiriciliği yapılan yonca (Medicago sativa L.) bitkilerinde 2019 yılında virüsleri... more Van ilinde yetiştiriciliği yapılan yonca (Medicago sativa L.) bitkilerinde 2019 yılında virüslerin oluşturduğu simptomlara benzer belirtiler görülmüştür. Gözlenen belirtiler arasında cüceleşme, yapraklarda mozaik deseni ve sararma, rozetlenme ve küçük yaprak oluşumu yer almaktadır. Simptom gösteren ve göstermeyen bitkilerden toplanan 19 yonca yaprak örneğine, virüs genomunu tespit edebilmek için uygun primer çiftleri ile RT-PCR testi uygulanmıştır. Yonca yaprağı örneklerinden şiddetli belirtiye sahip altısı beklenen büyüklükte 700 bp DNA band oluşturmuştur. Bunlar arasından rastgele seçilen ikisi bir plazmid vektörüne klonlanmıştır. Elde edilen rekombinant plazmidler her iki yönde dizilenmiştir. Dizi analizi sonuçlarına göre infekteli yoncalardaki virüsün Yonca mozaik virüs olduğu açığa çıkarılmıştır. Dizi bilgileri MT210179 ve MT210178 erişim numaraları ile gen bankasına yüklenmiştir ve sırasıyla Alakoy Y9 ve Alakoy Y1 olarak isimlendirilmiştir. Her iki dizi için gen bankasına kayıtlı 16 AMV dizisi ile oluşturulan filogenetik ağaca göre, her iki izolat da nükleotit düzeyinde ABD, Brezilya ve Puglia izolatları ile en yüksek benzerlik ve Güney Kore izolatı ile en düşük benzerlik oranı göstermiştir. Ayrıca her iki dizinin birbirleri arasında, 7 nükleotit değişikliği ile %98.45 oranında nükleotit benzerliği gösterdiği ortaya çıkarılmıştır. Gerçekleştirilen litaratür tarama çalışmalarına göre, bu çalışma Türkiye'nin Van ilinde yetiştirilen yonca bitkilerindeki Yonca mozaik virüsü (AMV)' nün ilk raporu ve moleküler analizidir.

Notulae Botanicae Horti Agrobotanici Cluj-Napoca

Seventy-eight tomato and pepper plants showing symptoms were tested for tomato spotted wilt ortho... more Seventy-eight tomato and pepper plants showing symptoms were tested for tomato spotted wilt orthotospovirus (TSWV) using specific primers targeting the full coat protein gene (CP) through RT-PCR. Plant samples were collected in Denizli region, Türkiye during September 2021. The PCR screening results revealed that 23 samples were infected with TSWV, indicating an infection rate of 29.48%. PCR products were subsequently sequenced bidirectionally, and the obtained sequences were deposited in GenBank under the accession numbers ON323583-84 for pepper, and OQ597214 for tomato. Phylogenetic analysis demonstrated a close relationship between the Turkish-Denizli TSWV isolates and previously reported isolates from tomato and pepper plants in Türkiye (KM407603), Hungary (KJ649612), and Serbia (GU369723). Moreover, in this study, three commercial chemicals and five selected phytochemicals were docked against the TSWV CP to assess their binding energies. The docking results indicate that the te...

Turkish Journal of Agriculture and Forestry, 2016

Marigold (Tagetes erecta L.) plants, also called Mexican or Aztec marigold, with symptoms of shoo... more Marigold (Tagetes erecta L.) plants, also called Mexican or Aztec marigold, with symptoms of shoot proliferation, dwarfing, and reddening were observed in ornamental gardens of Van Province (Turkey). Five plants, two of them showing reddening and three symptomless plants, were sampled at the end of September 2014. Genomic DNA isolated from symptomatic and nonsymptomatic plant leaves was used to amplify 16S rDNA fragments by nested polymerase chain reaction (PCR). Of the 5 marigold samples tested by PCR, only the two showing reddening symptoms yielded the expected 1.2-kb DNA fragments. Amplified PCR fragments were cloned into a plasmid vector and transformed into competent Escherichia coli strain JM 109. Recombinant plasmid DNA was isolated and sequenced bidirectionally. The provided sequences were 1244 bp and 1245 bp in length and were designated as isolate 1 and isolate 2, respectively. BLAST analysis of the 16S rDNA sequence and virtual restriction fragment length polymorphism (RFLP) analysis confirmed the presence of the phytoplasma "Candidatus Phytoplasma solani". The in silico virtual RFLP pattern of isolate 1, based on the 16S rDNA F2n/R2 fragment, was identical (similarity coefficient 1.00) to the reference pattern of 16Sr group XII, subgroup A (GenBank accession no.: AF248959). Isolate 1 was identified as a member of 16SrXII-A. Based on the same analyses, isolate 2 showed molecular characteristics different from reference patterns of all previously established 16Sr groups and subgroups. The most similar was the reference pattern of 16Sr group XII, subgroup A (GenBank accession no.: AF248959), with a similarity coefficient of 0.97. This is the first report of naturally occurring "Ca. P. solani" affecting T. erecta, which shows that this plant species is an alternate host of the agent.

Türkiye tarımsal araştırmalar dergisi, Jul 16, 2023

Bean (Phaseolus vulgaris L.) is one of the world's oldest crops with both financial and nutri... more Bean (Phaseolus vulgaris L.) is one of the world's oldest crops with both financial and nutritional importance. Bean common mosaic potyvirus (BCMV) is one of the prevalent viral agents that affect beans across the globe. Determining the presence of the agent in the relevant region is critical for minimizing crop losses by implementing appropriate preventive and control measures. In this study, 73 bean leaf samples were collected from bean-growing areas in the Denizli province of Türkiye in 2022. The samples were screened for the presence of viral agents using Polymerase Chain Reaction (PCR) with specific primers targeting the polypeptide gene. 26 of the bean samples were found to be positive for BCMV. The coat protein gene sequences of two randomly selected positive isolates were sequenced and deposited in the GenBank with accession numbers OQ910196 and OQ910197. The nucleotide sequences of isolates were found to have high similarity with those of isolates identified in various regions of the world. Phylogenetic analysis indicated that these isolates from Denizli, Türkiye were closely related to other Turkish isolates. However, since some Turkish isolates in the cluster associated with the Denizli isolates were identified as belonging to the US-5 or NL-6 strain, the current sequences may be related to these strains. Further research is necessary to identify the exact strain of the Denizli isolates, which could be achieved through the use of a strain differentiation set.

Emirates Journal of Food and Agriculture

A survey of yellow dwarf viruses (YDVs) -associated diseases of wheat plants was performed for th... more A survey of yellow dwarf viruses (YDVs) -associated diseases of wheat plants was performed for the first time in the Şırnak Province, Turkey. In plants wheat cultivated areas, symptoms such as diminished leaf size, dwarfing, yellowing, and reddening of leaves wheat plants were observed in cultivated areas. A total of 441 specimens were collected regardless of showing symptoms and assayed for Barley/Cereal Yellow Dwarf Viruses [B/CYDV] association by PCR tests using virus coat protein gene (CPG)-specific primer pairs. These assays demonstrated that 13.38% (55 samples) were positive to the occurrence of BYDV-PAV (9.73%) and CYDV-RPV (0.73%) for wheat viruses, but no BYDV-MAV, -SGV, and -RMV infections of BYDVs were found in PCR assays of collected samples. In addition, double infection of BYDV-PAV and CYDV-RPV was detected in 12 samples with a 2.91% infection rate. The CPG sequences of randomly selected two isolates were revealed using bacterial cloning and sequencing. Sequences obtai...

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi

Phytoplasmas are dangerous bacteria severely infecting agricultural production worldwide. In the ... more Phytoplasmas are dangerous bacteria severely infecting agricultural production worldwide. In the present study, the identification of phytoplasmas infecting tomato plants showing symptoms such as small leaves, flower abnormalities, stunting, witches' broom, and reddening was performed. Five plants, two symptomatic and three asymptomatic, were tested to verify phytoplasma infection. Total DNA isolated from 5 leaf samples was used as a template for PCR reactions. The phytoplasma agents were confirmed in the two symptomatic samples. BLASTn search of 16S rRNA of two sequences shared identity similarity of 99.84% with ‘Candidatus Phytoplasma australasia’. Computer-simulated virtual RFLP profiles show that the 16S rRNA sequences is identical to the reference pattern of the 16SrII-D subgroup, with a similarity coefficient of 1.00. Based on BLAST, virtual RFLP, and phylogenetic dendrogram, the identified phytoplasma strains are enclosed in the 16SrII-D subgroup. This is the first report...

Journal of the Institute of Science and Technology

Viruses infecting honey bees are diseases that cause infection and economic damage in every devel... more Viruses infecting honey bees are diseases that cause infection and economic damage in every developmental stage of honey bees all over the world. In this study, a survey was conducted to determine the presence and prevalence of two worldwide common honeybee viruses (deformed wing virus [DWV] and chronic bee paralysis virus [CBPV]). 128 apiaries from 9 different localities in the province of Bingöl were visited to determine viral RNA. Collected 384 honey bee samples were tested molecularly (reverse-transcriptase polymerase chain reaction, RTPCR) using genome-specific primers specific to each virus. In molecular tests, 28 of 128 apiaries (21.87%) gave a positive reaction for DWV, but no CBPV pathogen was detected in any apiary. The 711 bp nucleotide sequence revealed by cloning one of the randomly selected positive samples was registered in the gene bank with the accession number MZ357973. According to the BLASTn analysis in the NCBI database, the nucleotide sequence of the DWV agent ...

Ege Üniversitesi Ziraat Fakültesi Dergisi

Objective: The objective of this study was to investigate the group/subgroup of phytoplasma agent... more Objective: The objective of this study was to investigate the group/subgroup of phytoplasma agent in peppers showing phytoplasma symptoms. Material and Methods: In this study, plants collected from Iğdır province in 2020 were analyzed using direct and nested PCR tests, and BLASTn, iphyClassifier, Mega 7, and pDRAW32 programs were used. Results: In the tests performed, approximately 1.2 kb of DNA fragments specific to phytoplasma were obtained. The 16S rRNA nucleotide sequence (1254 bp in length) (OM663745) revealed that it was showed more than 99.44% nucleotide similarity to other ‘Ca. P. trifolii’ members. The tentative RFLP and phylogenetic analyzes performed proved the ‘Ca. P. trifolii’ the infection from the Clover proliferation group (16SrVI) group and subgroup A in symptomatic pepper plants. Conclusion: The presence of ‘Ca. P. trifolii’ in naturally infected peppers in Iğdır province of Turkey was detected using PCR-RFLP and cladistic analysis.

Journal of Apicultural Science

In this study, we conducted a six-month survey to evaluate the current status of three common hon... more In this study, we conducted a six-month survey to evaluate the current status of three common honey bee viruses (black queen cell virus [BQCV], acute bee paralysis virus [ABPV], and sacbrood virus [SBV]) in Turkey’s Bingöl region and revealed their phylogenetic relationships with the same types of viruses in other parts of the world. We randomly sampled 384 worker honey bees from a total of 128 apiaries from different locations of this region. Molecular tests confirmed the presence of SBV and BQCV, with infection rates of 7.03% and 11.7%, respectively, but ABPV could not be detected in any of the surveyed apiaries. In addition, double infection was detected in an apiary with an infection rate of 0.78%. The sequences of a partial polyprotein gene region of a randomly selected isolate from each detected virus were collected and registered in GenBank under the accession numbers MZ357971 and MZ357972 for SBV and MZ357974 for BQCV. The nucleotide sequence similarity of Turkish BQCV and S...

Turkish Journal of Agricultural and Natural Science, Dec 16, 2021

European Journal of Science and Technology, 2022

Kabak (Cucurbita pepo L.), Türkiye'nin tüm coğrafi bölgelerinde yetiştirilen önemli bir üründ... more Kabak (Cucurbita pepo L.), Türkiye'nin tüm coğrafi bölgelerinde yetiştirilen önemli bir üründür. Zucchini yellow mosaic virus (ZYMV), kabakgiller (Cucur-bitaceae) familyasının tüm türlerini etkilemekte ve yıkıcı etkisinden dolayı bü-yük ekonomik zararlara neden olmaktadır. Kabak türleri ve genotipleri, ZYMV'ne dayanıklılık için uzun süredir dünyanın birçok bölgesinde taranmak-tadır. Literatürde ZYMV'ye dayanıklı genetik kaynaklar rapor edilmiş olsa da, gerçekte bu kaynakların virüsün kimi şiddetli ırklarına karşı dayanıksız oldukları bildirilmektedir. Bu nedenle yürütülen bu çalışma ile ZYMV'ye dayanıklılık gösteren kabak çeşitlerinin veya genotiplerinin sayısının arttırılması hedeflen-miştir. Çalışmada 2005 yılında Kırşehir, Kayseri, Sakarya, Tekirdağ, Nevşehir ve Konya'dan toplanan genotipler kullanılmıştır. 2006 ve 2010 yılları arasında bu genotiplerin kedilenmesi ve seleksiyonu gerçekleştirilmiş ve S5 generasyon-ları üretilmiştir. Yüksek verimli, albenisi yük...

European Journal of Science and Technology, 2022

Ribosome-inactivating proteins (RIPs) are one of the enzymes that inhibit protein synthesis after... more Ribosome-inactivating proteins (RIPs) are one of the enzymes that inhibit protein synthesis after depurination of a specific adenine in ribosomal RNA. The tritin is one of type I RIPs that include RNA-N glycosidase domain from RIP family. In the present study, cDNA encoding tritin from leaves of wheat Kutluk-94 cultivar was isolated and cloned into pGEM-T Easy vector. The recombinant plasmid was sequenced. The different bioinformatics tools were used for assessment of tritin protein characteristics. A total of 38 tritin-like sequences were identified in some monocot plants. Results showed that tritin protein have conserved domain (Ricin-A) found in other RIPs associated with RNA N-glycosidase activity and shows chancing homology to the RIPs in other plant species. According to multiple sequence alignment, tritin has conserved amino acids which are crucial role in RNA N-glycosidase activity. Our study illustrates that results obtained from in silico analyses could provide a perspective to another researcher about molecular and structural properties of tritin protein.

Plant Protection Science, 2021

Phytoplasma-like symptoms of leaf yellowing and calyx malformation were observed in eggplant (Sol... more Phytoplasma-like symptoms of leaf yellowing and calyx malformation were observed in eggplant (Solanum melongena L.), upward leaves and fruit malformation in pepper (Capsicum annuum L.), and aerial tuber formation in potato (S. tuberosum L.) during the survey performed in the late season (August to September) of 2015 and 2016 in Van province (Turkey). A total of 100 samples were tested by nested-PCR using universal primer pairs to assess the sanitary status of the solanaceous crops and to characterise the phytoplasma isolates. Among them, seven samples resulted in a 1.25 kb DNA fragment, and five (two eggplants, two peppers, and one potato) were molecularly characterised (Accession No.: KY579357, KT595210, MF564267, MF564266, and MH683601). BLAST and the virtual restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes revealed the presence of two distinct phytoplasma infections in solanaceous crops: ‘Candidatus Phytoplasma trifolii’ a member of the clover proliferat...

ISPEC Journal of Agricultural Sciences, 2021

Fusarium spp is one of the major phytopathogenic microfungus strains causing severe losses in man... more Fusarium spp is one of the major phytopathogenic microfungus strains causing severe losses in many economically cultivated crops. The soil-borne pathogen Fusarium solani has historically been considered a serious agent across the globe, causing vascular wilt and root rot in agroeconomic crops and eventually leading to plant death. Three different concentrations (1 µl, 2 µl, and 4 µl) of essential oils (EO) extracted from lavender (Lavandula officinalis L.) and summer savory (Satureja hortensis L.) plants were mixed separately with PDA medium, and their antifungal effect against F. solani was investigated in vitro. When the results of the experiment were evaluated statistically, it was determined that the increasing concentrations of summer savory essential oil repressed the mycelial growth of the fungus, while lavender oil did not have any positive or negative effects. The inhibition activity of summer savory EO on F. solani was calculated as 43, 53, and 90% at the concentrations of...

Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 2021

Tomato plants displaying severe fruit deformation, flower sterility, aerial rooting, purplish lea... more Tomato plants displaying severe fruit deformation, flower sterility, aerial rooting, purplish leaves and leaf rolling were observed in tomato fields at Van province (Turkey). Samples were collected and total DNA was extracted from symptomatic and asymptomatic plants. Nested polymerase chain reaction (nested-PCR) assays were performed to amplify 16S rDNA sequences for molecular detection using universal primer pairs. Out of 100 tested tomato samples, 11% of tomato samples yielded a DNA fragment of 1.25 kb. Amplified PCR products were then cloned into pGEM T-Easy vector and sequenced using new generation DNA sequencing (NGS) system. The virtual restriction fragment length polymorphism (RFLP) analysis of 16S rDNA sequences and molecular detections were allowed to characterize possible phytoplasmas associated with diseased plants. Our results revealed the presence of two phytoplasma species belonging to two different ribosomal groups; ‘Candidatus Phytoplasma trifolii’ (16Sr VI-A group) ...