The colinear alignment of the genomes of papovaviruses JC, BK, and SV40

The DNAs of polyomaviruses JC, BK, and SV40 were analyzed, under a range of nonstringent hybridization conditions, for nucleotide sequence homology. When the hybridizations were performed at T m - 36°, conditions which would detect regions of homology with as much as 26% base mismatch, extensive homology was detected in all gene regions between the JC genome and both BK and SV40 DNAs. The regions of strongest sequence homology between these genomes formed stable duplexes at T m - 21°, indicating at least 85% base match. By two-dimensional cross-hybridization of restriction endonuclease cleavage fragments of JC to both those of BK and SV40 under nonstringent conditions, it was possible to map the homologous DNA fragments of each pair of viruses with respect to each other. The physical maps of these polyomaviruses could be colinearly aligned using the conserved single Eco RI site in each genome as the 0 map position. The region of strongest homology among these three genomes was localized in a narrow segment (0.76 to 0.85 map unit) in the late region, which in the SV40 genome contains the codons for the N-terminal half of the minor viral protein VP2.