Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

Abstract

Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

“…To investigate the possibility of endogenization of mitoviral sequences into the host genome (Liu et al, 2010;Chiba et al, 2011), we used three different mitovirus primer pairs and total cellular DNA from the host fungus as a template for PCR. The presence of mitochondrial DNA was verified with PCR amplification using the primer pair ML1/ ML2, which is specific for mitochondrial large subunit rDNA (White et al, 1990).…”

A Novel Victorivirus from a Phytopathogenic Fungus, Rosellinia necatrix, Is Infectious as Particles and Targeted by RNA Silencing

“…1D), and Mfold (43) was used for detection of the stem-loop hairpin downstream of the pentamer. Phylogenetic analysis was performed as described by Chiba et al (34). An amino acid sequence spanning the conserved RdRp motifs (I to VIII) of RnVV1 (amino acid positions 244 to 582, adopted from Bruenn [44]), and related sequences from selected members of the Totiviridae were extracted and aligned using the online version of MAFFT version 6 (45).…”

“…Due to the lack of effective control measures, virocontrol (biological control) of the disease using mycoviruses that attenuate the fungal virulence is an attractive option (13,29,30). To this end, an extensive search of a large number of field isolates was conducted allowing the detection of diverse dsRNA viruses such as a bipartite dsRNA virus, Rosellinia necatrix megabirnavirus 1 (RnMBV1), a quadrivirus, Rosellinia necatrix quadrivirus 1 (RnQV1), the reovirus mycoreovirus 3 (MyRV3), and the Rosellinia necatrix partitiviruses 1 and 2 (RnPV1 and RnPV2) (13,17,(31)(32)(33)(34)(35). Some of these viruses were shown to be able to confer hypovirulence under laboratory conditions.…”

First evidence for the existence of pennate diatom viruses

“…A recent study showed evidence for a horizontal gene transfer event from non-retroviral RNA viruses into the genomes of distantly related plant lineages (Chiba et al, 2011), suggesting that lateral gene transfer could occur through viral infections. The understanding of pennate and centric diatom viruses may elucidate their hosts' phylogenetic relationships and evolution.…”