Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey
Molecular 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 samp...
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Elsevier
2022
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| author | Morca, Ali Ferhan Çelik, Ali Coşkan, Sevgi Santosa, Adyatma Irawan Akbaş, Birol |
| author_facet | Morca, Ali Ferhan Çelik, Ali Coşkan, Sevgi Santosa, Adyatma Irawan Akbaş, Birol |
| author_sort | Morca, Ali Ferhan |
| collection | UGM |
| description | Molecular 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, Bartın, 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 ω 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. |
| first_indexed | 2024-03-13T23:58:24Z |
| format | Article |
| id | oai:generic.eprints.org:277297 |
| institution | Universiti Gadjah Mada |
| last_indexed | 2024-03-13T23:58:24Z |
| publishDate | 2022 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oai:generic.eprints.org:2772972022-05-24T00:38:52Z https://repository.ugm.ac.id/277297/ Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey Morca, Ali Ferhan Çelik, Ali Coşkan, Sevgi Santosa, Adyatma Irawan Akbaş, Birol Horticultural Crop Protection (Pests Diseases and Weeds) Molecular 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, Bartın, 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 ω 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. Elsevier 2022 Article PeerReviewed Morca, Ali Ferhan and Çelik, Ali and Coşkan, Sevgi and Santosa, Adyatma Irawan and Akbaş, Birol (2022) Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey. Physiological and Molecular Plant Pathology, 118. p. 101786. ISSN 08855765 http://dx.doi.org/10.1016/j.pmpp.2022.101786 doi:10.1016/j.pmpp.2022.101786 |
| spellingShingle | Horticultural Crop Protection (Pests Diseases and Weeds) Morca, Ali Ferhan Çelik, Ali Coşkan, Sevgi Santosa, Adyatma Irawan Akbaş, Birol Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title | Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title_full | Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title_fullStr | Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title_full_unstemmed | Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title_short | Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Turkey |
| title_sort | population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato pepper and chenopodium album in turkey |
| topic | Horticultural Crop Protection (Pests Diseases and Weeds) |
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