Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission
An 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...
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| Format: | Article |
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MDPI AG
2023-09-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/10/2434 |
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| author | Fereshteh Esmaeilzadeh Adyatma Irawan Santosa Ali Çelik Davoud Koolivand |
| author_facet | Fereshteh Esmaeilzadeh Adyatma Irawan Santosa Ali Çelik Davoud Koolivand |
| author_sort | Fereshteh Esmaeilzadeh |
| collection | DOAJ |
| description | An 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 <i>Solanum lycopersicum</i> and <i>Nicotiana rustica</i>. 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. |
| first_indexed | 2024-03-10T21:02:50Z |
| format | Article |
| id | doaj.art-a7621d76dcf34738a7478d316ce58b25 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:02:50Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-a7621d76dcf34738a7478d316ce58b252023-11-19T17:26:43ZengMDPI AGMicroorganisms2076-26072023-09-011110243410.3390/microorganisms11102434Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical TransmissionFereshteh Esmaeilzadeh0Adyatma Irawan Santosa1Ali Çelik2Davoud Koolivand3Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, IranDepartment of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, IndonesiaDepartment of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, TurkeyDepartment of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, IranAn 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 <i>Solanum lycopersicum</i> and <i>Nicotiana rustica</i>. 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.https://www.mdpi.com/2076-2607/11/10/2434experimental plant hostsgenetic ancestrymechanical transmissionphylogenypopulation geneticsselection constraint |
| spellingShingle | Fereshteh Esmaeilzadeh Adyatma Irawan Santosa Ali Çelik Davoud Koolivand Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission Microorganisms experimental plant hosts genetic ancestry mechanical transmission phylogeny population genetics selection constraint |
| title | Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission |
| title_full | Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission |
| title_fullStr | Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission |
| title_full_unstemmed | Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission |
| title_short | Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission |
| title_sort | revealing an iranian isolate of tomato brown rugose fruit virus complete genome analysis and mechanical transmission |
| topic | experimental plant hosts genetic ancestry mechanical transmission phylogeny population genetics selection constraint |
| url | https://www.mdpi.com/2076-2607/11/10/2434 |
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