Patterns of nucleotide sequence variation among cauliflower mosaic virus isolates.
A consensus nucleotide sequence of the DNA of nine isolates of cauliflower mosaic virus (CaMV) was used to examine variation of nucleotide sequence in CaMV. Variability in coding regions was lowest in open reading frames (ORFs) 1, 2, 3 and 5 and higher in ORFs 4 and 6. Silent substitutions were not uniformly distributed among the ORFs. The large intergenic region was also variable, particularly in loops and bulges of a predicted secondary structure for this region of the 35S RNA transcript. A profile of frequencies of the substitution of consensus nucleotides with other nucleotides revealed a deficit of A to G transitions and an excess of transversions involving A. Most insertions/deletions could be accounted for by template misalignment during replication. The results suggest that the major source of variation in CaMV DNA sequences is associated with replication by reverse transcription.
Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater 74078-0454.
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Chenault
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Melcher
D001482:Base Composition; D001483:Base Sequence; D017796:Caulimovirus / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D016384:Consensus Sequence; D004261:DNA Replication; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D017384:Sequence Deletion
D004279:DNA, Viral