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.
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.
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: