Identification of a distinct strain of Cotton leaf curl Gezira virus infecting tomato in Oman

Tomato ( Solanum lycopersicum ) plants exhibiting yellowing, curling and stunting symptoms were identified in fields of the Tawoos Agricultural Systems, in Al‐Batinah in Oman. Cloning and sequencing of restriction endonuclease digested rolling circle amplified viral DNA identified a cotton begomovirus (family Geminiviridae ) associated with the symptomatic tomato plants. Detailed analysis of complete sequences showed the virus to be a previously unknown strain of Cotton leaf curl Gezira virus (CLCuGeV) in association with the betasatellite Tomato leaf curl betasatellite (To LCB ). The new CLC uGeV strain, for which the name “Al Batinah” strain is suggested, has the greatest levels of sequence identity (91.9%) to an isolate of CLC uGeV recently reported from the neighbouring United Arab Emirates. Additionally, CLC uGeV‐Al Batinah was shown to have a recombinant origin with sequences donated by an African cassava mosaic virus ‐like parent. This is the first identification of this Malvaceae ‐adapted begomovirus in tomato. Although To LCB is common in Oman, being one of only two betasatellites identified there so far, this is the first identification of this betasatellite with CLC uGeV. The significance of these findings is discussed.