Genomic heterogeneity of rice dwarf phytoreovirus field isolates and nucleotide sequences of variants of genome segment 12

Abstract

Electrophoretic profiles of the dsRNAs of field isolates of rice dwarf virus (RDV) were compared with those of an isolate maintained at Hokkaido University (RDV-H). Unexpectedly, the genomic dsRNAs of most of the field isolates showed distinct electrophoretic mobility profiles. This was the case even among isolates from the same region. Genome segment 12 (S12) from some variants migrated faster than S12 from RDV-H. These RNAs were converted to full-length cDNAs and sequenced. S12 from all the variants had the same length of 1066 nucleotides with nucleotide sequence identities of 96 to 99%. Three open reading frames previously reported were present in all the variants, and the sequence identities were 95 to 99% for P12, 98 to 100% for P12OPa, and nearly 100% for P12OPb. A comparison of the nucleotide and amino acid sequences of the variants with sequences of the RDV-H and Akita isolate showed that there are two genomic types, one represented by RDV-H and the other by the Akita isolate.