Sequence Changes in Six Variants of Rice Tungro Bacilliform Virus and Their Phylogenetic Relationships

Azzam, Ossmat, Cabauatan, Pepito Q., Melcher, Ulrich, Ishikawa, Koichi, Omura, Toshihiro, Hibino, Hiroyuki, & Koganezawa, Hiroki (1999) Sequence Changes in Six Variants of Rice Tungro Bacilliform Virus and Their Phylogenetic Relationships. Journal of General Virology, 80(8), pp. 2229-2237.

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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.

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13 citations in Scopus
12 citations in Web of Science®
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ID Code: 39809
Item Type: Journal Article
Refereed: Yes
Additional URLs:
Keywords: Sequence changes, Six variants, Rice tungro bacilliform virus, phylogenetic relationships
ISSN: 0022-1317
Subjects: Australian and New Zealand Standard Research Classification > AGRICULTURAL AND VETERINARY SCIENCES (070000) > HORTICULTURAL PRODUCTION (070600)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Deposited On: 04 Apr 2011 22:17
Last Modified: 17 Jul 2017 04:34

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