title: Characterization of small interfering RNAs derived from Rice black streaked dwarf virus in infected maize plants by deep sequencing.
abstract: Rice black streaked dwarf virus (RBSDV) is the casual agent of maize rough dwarf disease, which frequently causes severe yield loss in China. However, the interaction between RBSDV and maize plants is largely unknown. RNA silencing is a conserved mechanism against viruses in plants. To understand the antiviral RNA interfering response in RBSDV-infected plants, the profile of virus-derived small interfering RNAs (vsiRNAs) from RBSDV in infected maize plants was obtained by deep sequencing in this study. Our data showed that vsiRNAs, accumulated preferentially as 21- and 22-nucleotide (nt) species, were mapped against all 10 genomic RNA segments of RBSDV and derived almost equally overall from both positive and negative strands, while there were significant differences in the accumulation level of vsiRNAs from segments 2, 4, 6, 7 and 10. The vsiRNAs (21 and 22 nt) generated from each segment of RBSDV genome had a 5'-terminal nucleotide bias toward adenine and uracil. The single-nucleotide resolution maps showed that RBSDV-derived siRNAs preferentially distributed in the 5'- or 3'-terminal regions of several genomic segments. In addition, our results showed that the mRNA levels of some components involved in antiviral RNA silencing pathway were differentially modified during RBSDV infection. Among them, the accumulation levels of ZmDCL1, ZmDCL2, ZmDCL3a, ZmAGO1a, ZmAGO1b, ZmAGO2a, ZmAGO18a and ZmRDR6 mRNAs were significantly up-regulated, while those of ZmDCL3b, ZmDCL4 and ZmAGO1c mRNAs showed no obvious changes in RBSDV-infected maize plants.
authors.affiliation: State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China.
authors.forename: Mingjun
authors.initials: M
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, 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 100193, China.
authors.forename: Zihao
authors.initials: Z
authors.lastname: Xia
authors.affiliation: Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China.
authors.forename: Dianping
authors.initials: D
authors.lastname: Di
authors.affiliation: Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China.
authors.forename: Aihong
authors.initials: A
authors.lastname: Zhang
authors.affiliation: Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China.
authors.forename: Hongqin
authors.initials: H
authors.lastname: Miao
authors.affiliation: State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, 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 100193, China. Electronic address: fanzf@cau.edu.cn.
authors.forename: Zaifeng
authors.initials: Z
authors.lastname: Fan
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D018506:Gene Expression Regulation, Plant; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics / Q000821:virology*; D010942:Plant Viruses / Q000235:genetics*; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D003313:Zea mays / Q000235:genetics / Q000821:virology*
chemical_list: D034741:RNA, Small Interfering; D012367:RNA, Viral
keywords: Deep sequencing; Fijivirus; RNA silencing; Rice black streaked dwarf virus; Virus-derived small interfering RNA