title: Characterization of small interfering RNAs derived from Sugarcane mosaic virus in infected maize plants by deep sequencing.
abstract: RNA silencing is a conserved surveillance mechanism against viruses in plants. It is mediated by Dicer-like (DCL) proteins producing small interfering RNAs (siRNAs), which guide specific Argonaute (AGO)-containing complexes to inactivate viral genomes and may promote the silencing of host mRNAs. In this study, we obtained the profile of virus-derived siRNAs (vsiRNAs) from Sugarcane mosaic virus (SCMV) in infected maize (Zea mays L.) plants by deep sequencing. Our data showed that vsiRNAs which derived almost equally from sense and antisense SCMV RNA strands accumulated preferentially as 21- and 22-nucleotide (nt) species and had an adenosine bias at the 5'-terminus. The single-nucleotide resolution maps revealed that vsiRNAs were almost continuously but heterogeneously distributed throughout the SCMV genome and the hotspots of sense and antisense strands were mainly distributed in the HC-Pro coding region. Moreover, dozens of host transcripts targeted by vsiRNAs were predicted, several of which encode putative proteins involved in ribosome biogenesis and in biotic and abiotic stresses. We also found that ZmDCL2 mRNAs were up-regulated in SCMV-infected maize plants, which may be the cause of abundant 22-nt vsiRNAs production. However, ZmDCL4 mRNAs were down-regulated slightly regardless of the most abundant 21-nt vsiRNAs. Our results also showed that SCMV infection induced the accumulation of AGO2 mRNAs, which may indicate a role for AGO2 in antiviral defense. To our knowledge, this is the first report on vsiRNAs in maize plants.
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Zihao
authors.initials: Z
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China; Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Zaifeng
authors.initials: Z
authors.lastname: Fan
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D010940:Plant Proteins / Q000235:genetics; D017800:Potyvirus / Q000235:genetics* / Q000502:physiology; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000235:genetics / Q000821:virology*
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D034741:RNA, Small Interfering