Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution.

Motoyuki Kunii,Hironori Nagano,Masanori Kanda,Yuji Kishima,Yoshio Sano,Ichiro Uyeda

doi:10.1186/1471-2164-5-80

Abstract

BackgroundPlant 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.ResultsWe 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.ConclusionsThese 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.

Highlights

Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences
Identification of RTBV-like sequences in the rice genomes Previously, we found a repetitive sequence near the rice waxy gene, which is partially homologous to the rice tungro bacilliform virus (RTBV) genome [12,17]
The segments of ERTBV were distributed throughout the rice genome

Summary

Introduction

Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. The endogenous viruses for banana streak virus (BSV) [6], tobacco vein-clearing virus (TVCV) [9] and petunia vein clearing-virus (PVCV) [4] could be activated as episomal viruses under certain conditions in the host plant, and appeared to have pathogenic potential The integrations of these viruses were shown to have been relatively recent events and the copy numbers of the endogenous virus sequences were found to be very low. For tobacco endogenous pararetroviruses (TEPRVs), it was estimated that there are about 1000 segments in the tobacco genome [8], but the intact virus has not been identified so far, suggesting that the integration of TEPRVs was not a recent event The finding of such endogenous virus sequences raises questions concerning 1) the integration process giving rise to endogenous virus sequences, 2) possible differences in the evolutionary rate between the virus and endogenous virus and 3) resistance potential as a result of endogenous virus integration

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