Tomato leaf curl Oman virus and associated Betasatellite causing leaf curl disease in tomato in Pakistan

Abstract

The ongoing global spread of Tomato yellow leaf curl virus (TYLCV) poses an endemic threat to tomato production in all tropical and sub-tropical regions of the world. In Oman, TYLCV evolved into the new species Tomato leaf curl Oman virus (ToLCOMV) by recombination with Papaya leaf curl virus (PaLCuV). In March 2017, during a field survey of Sindh province of Pakistan, tomato (Solanum lycopersicum L.) plants showing typical symptoms of Tomato leaf curl disease (ToLCD); such as leaf curling, yellowing and stunted plant growth were observed. For identification and characterization of the causative agent, leaf samples were collected and tested for the presence of begomoviruses and associated DNA satellites. We have recently reported the presence of ToLCOMV-PK (previously known as TYLCV-PK strain) on Cyamopsis tetragonoloba in the same province of Pakistan. The tomato samples were analyzed for the presence of ToLCOMV-PK using specific primers. Approx. 2.8 kb and 1.4 kb PCR products were obtained which were cloned and sequenced; the results indicated the presence of ToLCOMV-PK and Tomato leaf curl betasatellite (ToLCB). We were also able to identify defective molecules of ToLCOMV-PK which were about half the size of the complete virus. Phylogenetic analysis and the sequence demarcation tool (SDT) showed that these are new isolates of ToLCOMV-PK (ToLCOMV-Pakistan strain) associated with ToLCB. Recombination analysis detected a strong recombination event in ToLCOMV-PK in which TYLCV (JQ928346) and PaLCuV (LT009400) were major and minor parents, respectively. We also corrected the classification of the previously identified distinct strain i.e. TYLCV-PK (TYLCV-Pakistan strain) into ToLCOMV-PK strain, based on our current analysis and classification. Biolistic inoculation of ToLCOMV-PK and associated ToLCB in Nicotiana benthamiana plants showed that coinfection with ToLCB resulted in enhanced symptoms and virus accumulation. This report of ToLCOMV-PK associated with ToLCB infecting tomato in Pakistan represents the widespread and vast host range of ToLCOMV and which poses serious threat to tomato production in Pakistan.