title: Comprehensive analysis of microRNA-Seq and target mRNAs of rice sheath blight pathogen provides new insights into pathogenic regulatory mechanisms.
abstract: MicroRNAs (miRNAs) are ∼22 nucleotide non-coding RNAs that regulate gene expression by targeting mRNAs for degradation or inhibiting protein translation. To investigate whether miRNAs regulate the pathogenesis in necrotrophic fungus Rhizoctonia solani AG1 IA, which causes significant yield loss in main economically important crops, and to determine the regulatory mechanism occurring during pathogenesis, we constructed hyphal small RNA libraries from six different infection periods of the rice leaf. Through sequencing and analysis, 177 miRNA-like small RNAs (milRNAs) were identified, including 15 candidate pathogenic novel milRNAs predicted by functional annotations of their target mRNAs and expression patterns of milRNAs and mRNAs during infection. Reverse transcription-quantitative polymerase chain reaction results for randomly selected milRNAs demonstrated that our novel comprehensive predictions had a high level of accuracy. In our predicted pathogenic protein-protein interaction network of R. solani, we added the related regulatory milRNAs of these core coding genes into the network, and could understand the relationships among these regulatory factors more clearly at the systems level. Furthermore, the putative pathogenic Rhi-milR-16, which negatively regulates target gene expression, was experimentally validated to have regulatory functions by a dual-luciferase reporter assay. Additionally, 23 candidate rice miRNAs that may involve in plant immunity against R. solani were discovered. This first study on novel pathogenic milRNAs of R. solani AG1 IA and the recognition of target genes involved in pathogenicity, as well as rice miRNAs, participated in defence against R. solani could provide new insights into revealing the pathogenic mechanisms of the severe rice sheath blight disease.
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Runmao
authors.initials: R
authors.lastname: Lin
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Liye
authors.initials: L
authors.lastname: He
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Jiayu
authors.initials: J
authors.lastname: He
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Peigang
authors.initials: P
authors.lastname: Qin
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Yanran
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an 625014, China.
authors.forename: Qiming
authors.initials: Q
authors.lastname: Deng
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Xiaoting
authors.initials: X
authors.lastname: Yang
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Shuangcheng
authors.initials: S
authors.lastname: Li
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Shiquan
authors.initials: S
authors.lastname: Wang
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Wenming
authors.initials: W
authors.lastname: Wang
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Huainian
authors.initials: H
authors.lastname: Liu
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya'an 625014, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Li
authors.affiliation: Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China.|Key Laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Zheng
keywords: gene expression; microRNA; milRNA-mRNA interaction; pathogenic mechanisms; rice sheath blight pathogen