Recombination profiles between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in laboratory and field conditions: evolutionary and taxonomic implications

Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus co-exist in tomato crops in Italy since 2002 and have reached an equilibrium, with plants hosting molecules of both species plus others recombinant being the most frequent case. Here we have studied recombination events in field samples, as well as in experimental co-infections, in which recombinants were detected as early as 45 days following inoculation. In both conditions recombination breakpoints were essentially absent in regions corresponding to open reading frames V2, CP and C4, while they reached the highest density in the 3'-terminal portion of ORF C3, next to the region where the two transcription units co-terminate. The vast majority of breakpoints were mapped at the antisense ORFs, giving support to the speculation that the rolling-circle-replication mechanism and the existence of sense and antisense ORFs on the circular genome may result in clashes between replication and transcription complexes.