Characterization of virus‐specific DNA forms from tomato tissues infected by tobacco leaf curl virus: evidence for a single genomic component producing defective DNA molecules

The DNA forms of a tobacco leaf curl virus (TLCV) isolate, from infected tomato in Japan were characterized. Probes specific to TLCV and tomato yellow leaf curl geminivirus (TYLCV) from Thailand detected virus‐specific single‐ and double‐stranded DNA equivalent to DNA A of the bipartite geminiviruses. Hybridization analysis and polymerase chain reaction failed to detect a DNA B. In addition to the genomic DNA, defective DNA molecules of approximately half genome length were detected, which were cloned at a unique HpaII site present in the conserved stem‐loop region. Analysis of the partial sequence of 20 independent clones of defective DNA demonstrated their origin from a DNA Alike component. The clone pTLSG 2 was sequenced completely, indicating a large deletion near the coat protein gene and several rearrangements in the replication‐associated protein (AC1) and the intergenic region (IR). This is a novel finding characterizing TLCV at the molecular level, from which it can be predicted as a distinct geminivirus possessing a single genomic component. Furthermore, in infected tomatoes, large amounts of a defective DNA accumulate that have retained cis‐elements essential for replication.