Comprehensive surveillance and population study on plum pox virus in Ankara Province of Turkey

Coşkan, Sevgi; Morca, Ali Ferhan; Akbaş, Birol; Çeli̇k, Ali; Santosa, Adyatma Irawan

doi:10.1007/s41348-022-00597-5

Cited by 10 publications

(6 citation statements)

References 44 publications

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“…Plant virus infections result in significant economic losses in the global agricultural sector (Lecoq and Katis, 2014;Coşkan et al, 2022;Topkaya et al, 2023). The primary focus of defensive strategies in plant virus control is on preventive measures, including the utilization of sanitarily certified propagating material and insect vector management (Fereres and Raccah, 2015;Golino et al, 2017).…”

Section: Discussion Discussion Discussionmentioning

confidence: 99%

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

DEMİREL,

GÜLLER,

USTA

et al. 2024

Not Bot Horti Agrobo

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In 2021, a study was conducted in the Denizli region of Türkiye to investigate the phylogenetic relationship and presence of alfalfa mosaic alfamovirus (AMV) infecting pepper plants exhibiting viral disease symptoms. A total of 57 samples were collected, of which twenty-four tested positive for AMV with reverse transcriptase polymerase chain reaction (RT-PCR) assays. Samples from pepper plants displaying virus symptoms gave positive bands on the agarose gel, while healthy plants yielded negative results. One of the positive samples was randomly selected, cloned and sequenced. This sequence of the Denizli AMV isolate (753 bp) was recorded in the GenBank database with accession number OQ845956. The nucleotide sequence showed a high nucleotide consensus of 97%-99% compared with the nucleotide sequences of the same variants from different origins in GenBank. According to the phylogenetic tree generated through the Neighbour Joining (NJ) method, this AMV isolate belongs to the same group as Iranian isolates from various of hosts. Furthermore, in silico docking analysis of the coat protein (CP) of the AMV isolate and promising 12 essential oil compounds was performed to enable potential antiviral drug development. Docking study showed that eucalyptol, eugenol and carvacrol can make important contributions to the advancement of drug-based strategies for the managing of plant viruses by interacting with the virus coat protein of high binding energies, -5.3, -5.2 and -5.0 kcal mol-1, respectively. Although the presence of AMV in Denizli province has been reported previously, this study reports the phylogenetic relationships and docking analysis of the new AMV isolate in pepper crops.

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Section: Discussion Discussion Discussionmentioning

confidence: 99%

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

DEMİREL,

GÜLLER,

USTA

et al. 2024

Not Bot Horti Agrobo

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“…The F ST value ranges between 0, which is describing strictly identical populations, to 1, which is describing totally distinct populations [ 32 , 34 ]. A high gene flow and large genetic isolation between tested populations are usually indicated by an F ST value of at least 0.33 [ 35 , 36 ].…”

Section: Methodsmentioning

confidence: 99%

Global Population Structure of Apple Mosaic Virus (ApMV, Genus Ilarvirus)

Çeli̇k

Morca²,

Coşkan³

et al. 2023

Viruses

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The 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 (FST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, ±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.

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“…The genetic differentiation and gene flow among populations were assessed using the K S *, K ST *, Z *, S nn , and F ST (fixation index) [ 52 ]. For panmictic populations, the F ST value was 0, while a ratio higher than 0.25 implies expanding genetic separation [ 53 , 54 ].…”

Section: Methodsmentioning

confidence: 99%

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Çeli̇k

Coşkan²,

Morca³

et al. 2022

Plants

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A 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 ω 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.

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Comprehensive surveillance and population study on plum pox virus in Ankara Province of Turkey

Cited by 10 publications

References 44 publications

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

Global Population Structure of Apple Mosaic Virus (ApMV, Genus Ilarvirus)

Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

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