title: Nicotiana small RNA sequences support a host genome origin of cucumber mosaic virus satellite RNA.
abstract: Satellite RNAs (satRNAs) are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS) transgene fused with a Cucumber mosaic virus (CMV) Y satellite RNA (Y-Sat) sequence (35S-GUS:Sat) was transcriptionally repressed in N. tabacum in comparison to a 35S-GUS transgene that did not contain the Y-Sat sequence. This repression was not due to DNA methylation at the 35S promoter, but was associated with specific DNA methylation at the Y-Sat sequence. Both northern blot hybridization and small RNA deep sequencing detected 24-nt siRNAs in wild-type Nicotiana plants with sequence homology to Y-Sat, suggesting that the N. tabacum genome contains Y-Sat-like sequences that give rise to 24-nt sRNAs capable of guiding RNA-directed DNA methylation (RdDM) to the Y-Sat sequence in the 35S-GUS:Sat transgene. Consistent with this, Southern blot hybridization detected multiple DNA bands in Nicotiana plants that had sequence homology to Y-Sat, suggesting that Y-Sat-like sequences exist in the Nicotiana genome as repetitive DNA, a DNA feature associated with 24-nt sRNAs. Our results point to a host genome origin for CMV satRNAs, and suggest novel approach of using small RNA sequences for finding the origin of other satRNAs.
authors.affiliation: CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia; School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia.
authors.forename: Kiran
authors.initials: K
authors.lastname: Zahid
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Zhao
authors.affiliation: CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia.
authors.forename: Neil A
authors.initials: NA
authors.lastname: Smith
authors.affiliation: CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Schumann
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Fang
authors.affiliation: CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia.
authors.forename: Elizabeth S
authors.initials: ES
authors.lastname: Dennis
authors.affiliation: School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia.
authors.forename: Ren
authors.initials: R
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Hui-Shan
authors.initials: HS
authors.lastname: Guo
authors.affiliation: CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia.
authors.forename: Ming-Bo
authors.initials: MB
authors.lastname: Wang
mesh_terms: D019401:Cucumber Mosaic Virus Satellite / Q000235:genetics*; D017799:Cucumovirus / Q000235:genetics* / Q000472:pathogenicity; D019175:DNA Methylation / Q000235:genetics; D020868:Gene Silencing; D018745:Genome, Plant; D005966:Glucuronidase / Q000235:genetics*; D006378:Helper Viruses / Q000235:genetics; D030821:Plants, Genetically Modified; D034741:RNA, Small Interfering; D017423:Sequence Analysis, RNA; D014026:Nicotiana / Q000235:genetics* / Q000821:virology; D019076:Transgenes
chemical_list: D019401:Cucumber Mosaic Virus Satellite; D034741:RNA, Small Interfering; D005966:Glucuronidase