Molecular analysis of the genome segments S1, S4, S6, S7 and S12 of a Rice gall dwarf virus isolate from Thailand; completion of the genomic sequence

• Published in: Archives of virology 2007-07, Vol.152 (7), p.1315-1322
• Main Authors: Moriyasu, Y, Maruyama-Funatsuki, W, Kikuchi, A, Ichimi, K, Zhong, B, Yan, J, Zhu, Y, Suga, H, Watanabe, Y, Ichiki-Uehara, T, Shimizu, T, Hagiwara, K, Kamiunten, H, Akutsu, K, Omura, T
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; 5' Untranslated Regions; Agricultural research; Amino Acid Sequence; Amino acids; Base Sequence; Biological and medical sciences; Cloning; Double-stranded RNA; Dwarf disease; Fundamental and applied biological sciences. Psychology; Genome, Viral; Genomes; Homology; Microbiology; Miscellaneous; Molecular Sequence Data; Nonstructural proteins; Nucleotide sequence; Nucleotides; Oryza - virology; Phytoreovirus; Plant Diseases - virology; Plasmids; Proteins; Reoviridae; Reoviridae - classification; Reoviridae - genetics; Reoviridae - isolation & purification; Rice; Rice dwarf virus; Rice gall dwarf virus; RNA polymerase; Sequence Homology, Amino Acid; Species Specificity; Structural proteins; Thailand; Tumors; Viral Proteins - genetics; Virions; Virology; Viruses; Wound tumor virus
• ISSN: 0304-8608; 1432-8798
• DOI: 10.1007/s00705-007-0948-7

The complete nucleotide sequences of the double-stranded RNA segments S1, S4, S6, S7 and S12 of the genome of a Rice gall dwarf virus (RGDV) isolate from Thailand were determined. The segments consisted of 4505, 2622, 1648, 1652 and 853 nucleotides, encoding putative proteins of 1458, 725, 489, 511 and 206 amino acids with molecular masses of approximately 166, 80, 53, 59 and 24 kDa, respectively. Homology searches indicated that each of the putative proteins has a counterpart in isolates of Rice dwarf virus (RDV) and Wound tumor virus, two other species in the genus Phytoreovirus. However, no similarities were found to other registered sequences, including those of other viruses that belong to the family Reoviridae. The identities between homologous structural proteins of RGDV and RDV ranged from 34 to 51% and were thus higher than those between homologous non-structural proteins of RGDV and RDV (16-37%). Among the nonstructural proteins, the highest amino acid sequence identity (37%) was observed for RGDV Pns11 and RDV Pns10, a constituent of tubular inclusions. This observation suggests that a specific amino acid backbone might be required for maintaining not only the three-dimensional structure of virions but also that of inclusions. The entire sequence of the RGDV genome is now available.