Sequence of subterranean clover stunt virus DNA: affinities with the geminiviruses

The nucleotide sequences of seven circular, single-stranded DNA components of one isolate of subterranean clover stunt virus (SCSV) have been determined. Each component, of about 1 kb, appears to encode a single open reading frame in the same sense as the encapsidated DNA. Notably, the proteins encoded by two SCSV components are related. Each has a consensus nucleotide binding motif and shares about 40% amino acid identity with the other and with the putative replication proteins of banana bunchy top virus and coconut foliar decay virus. The noncoding regions of the five other SCSV components share a highly conserved noncoding sequence of about 160 nucleotides. All seven components were found to contain a sequence capable of forming a stable stem-loop structure in the noncoding region which contains a conserved 9-nucleotide sequence in the loop, very similar to that of the geminiviruses. In addition, the putative replication proteins of SCSV are similar to those of the geminiviruses. We suggest that the SCSV-like viruses and the geminiviruses share a common ancestor and that this ancestor was more like SCSV in particle structure and genome organisation.