title: High-throughput sequence analysis of small RNAs in grapevine (Vitis vinifera L.) affected by grapevine leafroll disease.
abstract: Grapevine leafroll disease (GLRD) is one of the most economically important virus diseases of grapevine (Vitis spp.) worldwide. In this study, we used high-throughput sequencing of cDNA libraries made from small RNAs (sRNAs) to compare profiles of sRNA populations recovered from own-rooted Merlot grapevines with and without GLRD symptoms. The data revealed the presence of sRNAs specific to Grapevine leafroll-associated virus 3, Hop stunt viroid (HpSVd), Grapevine yellow speckle viroid 1 (GYSVd-1) and Grapevine yellow speckle viroid 2 (GYSVd-2) in symptomatic grapevines and sRNAs specific only to HpSVd, GYSVd-1 and GYSVd-2 in nonsymptomatic grapevines. In addition to 135 previously identified conserved microRNAs in grapevine (Vvi-miRs), we identified 10 novel and several candidate Vvi-miRs in both symptomatic and nonsymptomatic grapevine leaves based on the cloning of miRNA star sequences. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of selected conserved Vvi-miRs indicated that individual members of an miRNA family are differentially expressed in symptomatic and nonsymptomatic leaves. The high-resolution mapping of sRNAs specific to an ampelovirus and three viroids in mixed infections, the identification of novel Vvi-miRs and the modulation of certain conserved Vvi-miRs offers resources for the further elucidation of compatible host-pathogen interactions and for the provision of ecologically relevant information to better understand host-pathogen-environment interactions in a perennial fruit crop.
authors: Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA.
authors: Olufemi J
authors: OJ
authors: Alabi
authors: Yun
authors: Y
authors: Zheng
authors: Guru
authors: G
authors: Jagadeeswaran
authors: Ramanjulu
authors: R
authors: Sunkar
authors: Rayapati A
authors: RA
authors: Naidu
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D029381:Closteroviridae / Q000235:genetics* / Q000302:isolation & purification; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D016679:Genome, Viral / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010935:Plant Diseases / Q000235:genetics / Q000821:virology*; D018515:Plant Leaves / Q000235:genetics / Q000821:virology; D018749:RNA, Plant / Q000235:genetics*; D012367:RNA, Viral / Q000145:classification / Q000235:genetics*; D015203:Reproducibility of Results; D014772:Viroids / Q000235:genetics / Q000302:isolation & purification; D027843:Vitis / Q000235:genetics* / Q000821:virology*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D012367:RNA, Viral