Genetic diversity and evolution of satellite RNAs associated with the bamboo mosaic virus.

Ing-Nang Wang,Sih-Min Yen,Wen-Bing Yeh,Yau-Heiu Hsu,Chung-Chi Hu,Ching-Wei Lee,Na-Sheng Lin,Aln Rao

doi:10.1371/journal.pone.0108015

Abstract

Satellite RNAs (satRNAs) are subviral agents that depend on cognate helper viruses for genome replication and encapsidation. Their negative impacts on helper viruses have been exploited to control plant viral diseases. SatBaMV is a commonly found satRNA associated with Bamboo mosaic virus (BaMV) that infects diverse bamboo species in the field. To investigate the genetic diversity and evolution of satRNAs, we examined seven satBaMV populations derived from five bamboo species and cultivars from Taiwan, China, and India and one from the greenhouse. We found 3 distinct clades among the seven populations. Clade I is consisted of all satBaMV isolates, except for those from Dendrocalamus latiflorus in Taiwan and Bambusa vulgaris in India, which belong to Clades II and III, respectively. Interestingly, nucleotide diversity was lower for Clade I than II and III. However, the nucleotide diversity did not seem to depend on bamboo species or geographic location. Our population genetic analyses revealed the presence of excessive low-frequency polymorphic sites, which suggests that the satBaMV population was under purifying selection and/or population expansion. Further analysis of P20, the only satBaMV gene that encodes a non-structural protein involved in the long-distance movement of satBaMV, showed evidence of purifying selection. Taken together, our results suggest that purifying selection against defective P20 protein is responsible at least in part for the evolution of the satBaMV genome.

Highlights

One of the most striking and under-appreciated differences between plant and animal viruses is the predominant association of satellite RNAs with the plant viruses [1,2,3]
Baseline error rate from RT-PCR To establish the baseline error rate introduced by RT-PCR, we used a plasmid-borne satBaMV cDNA as the template to generate RNA transcripts with the T7 RNA polymerase, followed by reverse transcription and PCR amplification under the same conditions used for field samples
With the commonly used dN/dS test implemented in MEGA [48], we found that 4 of the 7 populations (i.e., B. vulgaris Schrader ex Wendland (Bvu), D. latiflorus Munro (Dl), D. latiflorus Munro cv. ‘‘Mei-nung’’ (DlM), and B. vulgaris from India (BvuI)) showed significantly smaller dN values than corresponding dS values (Table 2), indicating the presence of purifying selection

Summary

Introduction

One of the most striking and under-appreciated differences between plant and animal viruses is the predominant association of satellite RNAs (satRNAs) with the plant viruses [1,2,3]. The genomes of satRNAs are small, usually ,1,500 nucleotides (nt) [1] Their sequences do not reveal any recognizable open reading frame (ORF) or show only a single ORF encoding a small protein. SatRNAs are commonly seen as molecular parasites [3,6] engaging in a zerosum game by exploiting vital functions provided by their helper viruses. One manifestation of this antagonistic interaction between satRNAs and their helper viruses is the attenuation of disease symptoms, presumably as a result of reduced viral titers in the host plants. One contributing factor to such variable interactions may be the fascinating interplay among three parties: the satRNA, the helper virus, and the host defense mechanisms, most notably the RNA silencing pathway [1]

Methods

Results

Conclusion