Full text

Turn on search term navigation

© 2011 Chiba et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Chiba S, Kondo H, Tani A, Saisho D, Sakamoto W, et al. (2011) Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes. PLoS Pathog 7(7): e1002146. doi:10.1371/journal.ppat.1002146

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.

Details

Title
Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes
Author
Chiba, Sotaro; Kondo, Hideki; Tani, Akio; Saisho, Daisuke; Sakamoto, Wataru; Kanematsu, Satoko; Suzuki, Nobuhiro
Section
Research Article
Publication year
2011
Publication date
Jul 2011
Publisher
Public Library of Science
ISSN
15537366
e-ISSN
15537374
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1289083272
Copyright
© 2011 Chiba et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Chiba S, Kondo H, Tani A, Saisho D, Sakamoto W, et al. (2011) Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes. PLoS Pathog 7(7): e1002146. doi:10.1371/journal.ppat.1002146