title: Characterization of complete genome and small RNA profile of pagoda yellow mosaic associated virus, a novel badnavirus in China.
abstract: A new badnavirus was discovered from pagoda trees showing yellow mosaic symptoms on the leaves by high throughput sequencing of small RNAs. The complete genome of this virus was determined to comprise 7424 nucleotides, and the virus shared 40.4-45.1% identity with that of other badnaviruses. The genome encodes five open reading frames (ORFs) on the plus strand, which includes three conserved badnaviral ORFs. These results suggest that this virus is a new member of the genus Badnavirus in the family Caulimoviridae. The virus is tentatively named pagoda yellow mosaic associated virus (PYMAV). Phylogenetic analysis suggested that this virus together with gooseberry vein banding virus (GVBV) and grapevine vein-clearing virus (GVCV) forms a separate group that is distinct two other well characterized badnaviral groups. Additionally, the viral derived small RNA (vsRNA) profile of PYMAV was analyzed and compared with that of viruses within the same family. Results showed that the most abundant PYMAV vsRNAs were 21-nt, whereas other viruses in the same family have a predominance of 22- or 24-nt vsRNA. The percentage of sense PYMAV vsRNA was almost equal to that of antisense vsRNA, whereas vsRNAs of other viruses in the family display preferences toward the sense strand of their genome. Furthermore, PYMAV vsRNAs were symmetrically distributed along the genome with no obvious vsRNA generating hotspots.
authors.affiliation: College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China.
authors.forename: Yilun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, Zhejiang, PR China; Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Cheng
authors.affiliation: College of Agriculture, Northeast Agricultural University, Key Laboratory of Soybean Biology, Ministry of Education, Harbin 150030, Heilongjiang, PR China.
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Wu
authors.affiliation: Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada.
authors.forename: Aiming
authors.initials: A
authors.lastname: Wang
authors.affiliation: College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China. Electronic address: wxy5551@126.com.
authors.forename: Xiaoyun
authors.initials: X
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D019195:Badnavirus / Q000235:genetics* / Q000302:isolation & purification; D002681:China; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D058727:RNA, Small Untranslated / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D029909:Sophora / Q000821:virology
chemical_list: D004279:DNA, Viral; D058727:RNA, Small Untranslated; D012367:RNA, Viral
keywords: Badnavirus; Genome; Pagoda; Phylogeny; Small RNA