Genetic diversity and phylogenetic analyses of tomato chlorosis virus isolates using the coat protein gene sequences

Since the first report of tomato chlorosis virus (ToCV) in 2008, yellowing symptoms were observed in major tomato production areas of Turkey. Therefore, surveys were conducted in Antalya, Burdur, Isparta and Muğla provinces where 329 symptomatic tomato samples were collected from greenhouses and open fields. Testing all samples by RT-PCR using primers specific for ToCV coat protein (CP) gene revealed that 113 of 329 tomato samples resulted in positive amplification of this virus. While ToCV was not detected in Isparta and Burdur, more than 50% of the samples collected from Antalya tested positive. The CP genes of 12 selected ToCV isolates from different areas were cloned, sequenced and compared with each other and the full-length CP genes of isolates from other countries. Genetic diversity and phylogenetic analysis showed that the Turkish ToCV isolates have low genetic diversity and they are closely related, clustering in the same phylogenetic group. On the other hand, the CP genes of ToCV isolates from different countries showed greater diversity than the Turkish isolates and were phylogenetically divided into three groups.