BACKGROUND: Plant genomes contain various kinds of repetitive sequences such as
transposable elements,
microsatellites,
tandem repeats and virus-like sequences. Most of them, with the
exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes
led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous
rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the
rice genome. Here, we reconstructed putative
virus structures from RTBV-like sequences in the
rice genome and characterized to understand evolutionary implication, integration manner and involvements of
endogenous virus segments in the corresponding disease response. RESULTS: We have collected ERTBVs from the
rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be
phylogenetically divided into three clusters. For each
phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of
DNA and
amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV
copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely
susceptible to RTBV. The
DNA methylation state of the ERTBV sequences was
correlated with their
copy number in the genome. CONCLUSIONS: These ERTBV segments are unlikely to have functional potential as a
virus. However, these sequences facilitate to establish putative
virus that provided information underlying
virus integration and evolutionary relationship with existing
virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of
endogenous virus segments against its related disease.
