Sequences of the CpCDPKV genome used to produce the hairpin-RNAi construct. The diagram shows the circular DNA genome of CpCDPKV. Shown are the open-reading frames (ORFs) V1 and V2 (encoding the coat protein and movement protein, respectively), in the virion-sense and the C1 and C2 (encoding the replication associated protein [Rep; from a spliced product of the C1 and C2 ORFs] and the Rep A [from the C1 ORF], respectively), as well as the intron spliced from a mRNA from which Rep is translated. The large intergenic (non-coding) region (LIR) sits between the C1 and V1 ORFs, whereas the small intergenic region (SIR) sits between the C2 and V2 ORFs. The LIR contains a predicted hairpin-loop structure which contains (within the sequence of the loop) the conserved (between geminiviruses) TAATATTAC sequence which forms part of the origin of virion-strand DNA replication. The position of the hairpin-loop structure is indicated by the black circle at position zero. The CpCDPK virus sequences (730 bp) used to produce the hairpin RNAi construct is shown by the grey arc; this spans the 5' Rep, LIR and 5' MP sequences.