Variation in the genome of rice tungro bacilliform virus: molecular characterization of six isolates

Abstract

The DNA genomes of isolates office tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.

A variable region of the Sugarcane Bacilliform Virus (SCBV) genome can be used to generate promoters for transgene expression in sugarcane

“…By performing a PstI digestion on this DNA pool or by designing PCR primers with a specific sequence of 18 bases, we have unintentionally selected for subsets within this large pool. Any study on badnavirus variation can no longer consider one isolate to be representative of the entire group, as considerable variation has been demonstrated for several badnaviruses (Fan et al 1996;Briddon et al 1999).…”

Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution

“…Previous study on phylogenetic relationships among six variants of RTBV from Philippines pointed out the greatest variation in the cysteinerich region of ORF3 [19]. However, all the RTBV isolates from within Indian subcontinent (SA type) were reported as homogenous [18,21]. Later, Nath et al [20] reported a deletion of 10 codons at the 3 0 -terminal part of ORF3 of AP isolate resulting in significant variations among the SA isolates.…”

“…Previous investigations, using DNA cross-hybridization, partial nucleotide sequencing and PCR amplification of the genomes of several RTBV isolates, concluded that RTBV isolates grouped into two clusters, known as 'South-east Asian' (SEA) type and 'South Asian' (SA) type [18]. Out of ten complete sequences of RTBV available in the database, eight are from SEA region represented by six isolates from Philippine [2,9,17,19], one from Malaysia [11] and one from Thailand.…”

“…The West Bengal (WB) and Andhra Pradesh (AP) isolates of RTBV from India represents the SA type [20]. The SA isolates of RTBV showed divergence from the SEA isolates due to several insertions, deletions and substitutions, mostly in the intergenic regions [18]. Previous study on phylogenetic relationships among six variants of RTBV from Philippines pointed out the greatest variation in the cysteinerich region of ORF3 [19].…”

Immunological characterization of rice tungro spherical virus coat proteins and differentiation of isolates from the Philippines and India

“…Therefore, it is apparent that differentiation of tungro strains cannot be based simply on the symptornatology. Sequence analysis and crosshybridization experiments have shown that there are basically two groups of RTBV isolates: one from the Indian subcontinent and the other from the Philippines and Malaysia (Fan et al, 1996). There have not been any serological studies on variation of tungro viruses.…”