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

Abstract

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 A-like 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.