title: Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships.
abstract: The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
authors.affiliation: Entomology and Plant Pathology Division, International Rice Research Institute, PO Box 933, 1099 Manila, Philippines1.
authors.forename: Pepito Q
authors.initials: PQ
authors.lastname: Cabauatan
authors.affiliation: Oklahoma State University, Stillwater, OK 74078, USA2.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Melcher
authors.affiliation: National Agriculture Research Center, Tsukuba 305-0856, Japan3.
authors.forename: Koichi
authors.initials: K
authors.lastname: Ishikawa
authors.affiliation: National Agriculture Research Center, Tsukuba 305-0856, Japan3.
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Omura
authors.affiliation: National Institute for Agroenvironmental Science, Tsukuba 305-8604, Japan4.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hibino
authors.affiliation: Shikoku National Agricultural Experiment Station, Zentsuji, Kagawa 765-0001, Japan5.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Koganezawa
authors.affiliation: Entomology and Plant Pathology Division, International Rice Research Institute, PO Box 933, 1099 Manila, Philippines1.
authors.forename: Ossmat
authors.initials: O
authors.lastname: Azzam
mesh_terms: D000595:Amino Acid Sequence; D019195:Badnavirus / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D004269:DNA, Bacterial; D015246:Deoxyribonuclease EcoRI; D015252:Deoxyribonucleases, Type II Site-Specific; D014644:Genetic Variation; D008969:Molecular Sequence Data; D016296:Mutagenesis; D012275:Oryza / Q000821:virology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011995:Recombination, Genetic; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D004269:DNA, Bacterial; D015246:Deoxyribonuclease EcoRI; C024388:CTGCAG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases