title: Genetic diversity and evolution of satellite RNAs associated with the bamboo mosaic virus.
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.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, Republic of China; Department of Biological Sciences, University at Albany, Albany, New York, United States of America.
authors.forename: Ing-Nang
authors.initials: IN
authors.lastname: Wang
authors.affiliation: Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, Republic of China.
authors.forename: Chung-Chi
authors.initials: CC
authors.lastname: Hu
authors.affiliation: Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, Republic of China.
authors.forename: Ching-Wei
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, Republic of China.
authors.forename: Sih-Min
authors.initials: SM
authors.lastname: Yen
authors.affiliation: Department of Entomology, National Chung Hsin University, Taichung, Taiwan, Republic of China.
authors.forename: Wen-Bing
authors.initials: WB
authors.lastname: Yeh
authors.affiliation: Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, Republic of China.
authors.forename: Yau-Heiu
authors.initials: YH
authors.lastname: Hsu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, Republic of China.
authors.forename: Na-Sheng
authors.initials: NS
authors.lastname: Lin
mesh_terms: D031723:Bambusa / Q000821:virology*; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics; D005843:Geography; D009029:Mosaic Viruses / Q000235:genetics* / Q000302:isolation & purification; D009711:Nucleotides / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D011110:Polymorphism, Genetic; D019244:RNA, Satellite / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D009711:Nucleotides; D019244:RNA, Satellite; D012367:RNA, Viral; D014764:Viral Proteins