title: Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection.
abstract: Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Jinyan
authors.initials: J
authors.lastname: Wang
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Wengui
authors.initials: W
authors.lastname: Yu
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Yuwen
authors.initials: Y
authors.lastname: Yang
authors.affiliation: College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Tianzi
authors.initials: T
authors.lastname: Chen
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Tingli
authors.initials: T
authors.lastname: Liu
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Na
authors.initials: N
authors.lastname: Ma
authors.affiliation: College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Yang
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.affiliation: Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Baolong
authors.initials: B
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D053839:Begomovirus / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development; D035683:MicroRNAs / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D016376:Oligonucleotides, Antisense / Q000378:metabolism; D010935:Plant Diseases / Q000821:virology; D062085:RNA, Long Noncoding / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D016376:Oligonucleotides, Antisense; D062085:RNA, Long Noncoding