The genomes of two Watermelon chlorotic stunt virus (WmCSV) isolates, one from the Sudan and one from Iran, were cloned and sequenced. Sequence relationship with other geminiviruses characterizes WmCSV as a typical Eastern Hemisphere geminivirus with a bipartite genome. The two geographically distant WmCSV isolates from Africa and the Middle East share a very high overall sequence similarity: 98% between their DNA-A and 96% between their DNA-B components, and their respective capsid proteins are identical. A single amino acid change in the capsid protein (N131D) renders WmCSV whitefly nontransmissible. This region of the capsid is also implicated in transmission by Bemisia tabaci of Tomato yellow leaf curl virus.

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Complete nucleotide sequence of the Iranian strain of tomato yellow leaf curl virus (TYLCV-IR) was determined and compared with some begomoviruses. The complete sequence of TYLCV-IR clustered together with TYLCV and TYLCV-MId from Israel. A similar relationship holds when the deduced amino acid sequences of V1, V2, C2 and C3 and nucleotide sequences of IR, and RIR were compared. In contrast, phylogenetic analyses of amino acid sequences of C4, C1, and nucleotide sequences of LIR revealed that TYLCV-IR clustered with TLCIRV and two Indian species: ToLCBV- [Ban4], and ToLCKV. The phylogenetic analyses, Recombination Detection Program analyses, and sequence alignment survey provided evidence of the occurrence of recombination between an Israeli TYLCV-MId, as major parent, and TLCIRV, as minor parent. In this recombination event, a region (from nt 2149 to 2766) of TYLCV-MId genome were replaced with corresponding genome sequences of TLCIRV (RDP P-value = 5.976 x 10(-72)), which include LIR, C4, and N-terminal of C1. Infectivity of the cloned TYLCV-IR genome was demonstrated by successful agroinoculation of tomato ( Lycopersicon esculentum) and other plant species. The disease was transmitted by the natural vector Bemisia tabaci from agroinoculated plants to test plants, reproducing in this way the full biological cycle and proving that the genome of TYLCV-IR consists of only one circular single-stranded DNA molecule.