43. DNA sequences homologous to rice tungro bacilliform virus (RTBV) present in the rice genome
  H. NAGANO, A. OKA, Y. KISHIMA and Y. SANO

Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan

We recently reported that a region near the Waxy (Wx) locus varies in copy number among closely related species of rice (Nagano et al. 1999, 2000). This variable region is homologous to the rice tungro bacilliform virus (RTBV) sequence.

The variable region is located about 55kb upstream of the Wx gene (Nagano et al. 2000) (Fig. 1). Three successive probes of this region gave discrete ladder patterns in Southern blots and different copy numbers among the AA-genome species (Nagano et al. 2000). Approximately 40 bands were observed in Oryza sativa, O. rufipogon, O. meridionalis and O. longistaminata, whereas O. glaberrima, O.barthii and O. glumaepatula gave only a few bands. The other regions within the 300-kb contig were unlikely to have such different copy numbers among the AA-genomes. We sequenced the corresponding 10-kb region and found homologies to the RTBV at two proximal sites (Nagano et al. 1998). The left side of the homologous region is 54.6% similar to a 1.2-kb segment in the beginning of ORFIII of the virus genome, and the right side homology is 59% similar to the end region of ORFIII (Fig. 1). The two sequences with homology to RTBV are oppositelty directed. Recently, the rice genome project disclosed annotated sequences of this region. According to the annotation, these two rice sequences were suggested to participate in the 5' region of independent open reading frames which are located on different strands and are functionally unknown (Fig. 1). We examined whether the similar hybridization patterns are reproduced when the homologous sequences in the RTBV genome were used as probes to the rice genome. It was then confirmed that the similar patterns were obtained by probing with the virus genome, and the

patterns were variable among the AA-genome species (data not shown).

RTBV is a pararetrovirus which encapsidates a double-stranded DNA genome replicated by reverse transcription of an RNA intermediate. Although plant viral sequences have generally been considered to rarely integrate into host genomes, several recent reports suggest that plant pararetrovirus DNA might integrate more often into host chromosomes (Jakowitsch et al. 1999, Harper et al. 1999, Ndowora et al. 1999). Our data also support this possibility due to RTBV fragments that were found in the Oryza genomes. It is of interest that the copy numbers of the RTBV-homologous fragment were highly variable among the Oryza species. This finding might give insight into the molecular basis of resistance to RTBV which causes a serious disease reducing the rice production in East Asia, as well as molecular mechanisms for integration and amplification of the virus genome in the plant genome.

The nucleotide sequence data for the corresponding region was reported by the rice genome project to the DDBJ, Gene Bank and EMBL Nucleotide Sequence Databases under the accession number AP000559.

References

Harper G., J.O. Osuji, J.S. Heslop-Harrison and R. Hull, 1999. Integration of banana streak badnavirus into the Musa genome: Molecular and cytogenetic evidence. Virology 255: 207-213.

Jakowitsch J., M.F. Mette, J. van der Winden, M.A. Matzke and A.J.M. Matzke, 1999. Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc. Natl. Acad. Sci. USA 96: 13241-13246.

Nagano H., S. Kawasaki, Y. Kishima and Y. Sano, 2000. Structural differences in the vicinity of the waxy locus among the Oryza species with the AA-genome: identification of variable regions. Theor. Appl. Genet. 100: 376-383.

Nagano H., Khin Thidar, A. Oka, Y. Kishima and Y. Sano, 1998. Structural analysis of highly variable region among rice species with AA-genome. Proceeding of the meeting in Fukuoka for The Molecular Biology Society of Japan 22: 277. (in Japanese)

Nagano H., L.-H. Wu, S. Kawasaki, Y. Kishima and Y. Sano, 1999. Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice. Genome 42: 1121-1126.

Ndowora T., G. Dahal, D. LaFleur, G. Harper, R. Hull, N.E. Olszewski and B. Lockhart, 1999. Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences. Virology 255: 214-220.