title: Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing.
abstract: MicroRNAs (miRNA) play key regulatory roles in diverse biological processes. Cynoglossus semilaevis is an important commercial mariculture fish species in China. To identify miRNAs and investigate immune-related miRNAs of C. semilaevis, we performed high-throughput sequencing on three small RNA libraries prepared from C. semilaevis immune tissues (liver, head kidney, spleen, and intestine). One library was prepared under normal conditions (control, CG); two were prepared during Vibrio anguillarum infection, where vibriosis symptoms were obvious and non-obvious (HOSG and NOSG, respectively). We obtained 11,216,875, 12,313,404, and 11,398,695 clean reads per library, respectively. Bioinformatic analysis identified 452 miRNAs, including 24 putative novel miRNAs. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. For NOSG-CG, there was significant differential expression of 175 (38.72%) miRNAs. There was significant differential expression of 215 (47.57%) miRNAs between HOSG and CG. Compared with CG, The HOSG-NOSG comparison revealed significantly different expression of 122 (26.99%) miRNAs respectively. Real-time quantitative PCR (RT-qPCR) experiments were performed for 10 miRNAs of the three samples, and agreement was found between the sequencing and RT-qPCR data. For miRNAs that were significantly differentially expressed, functional annotation of target genes by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that a set of miRNAs that were expressed highly abundantly and significantly differentially were might involved in immune system development and immune response. To our understanding, this is the first report of comprehensive identification of C. semilaevis miRNAs being differentially regulated in immune tissues (liver, head kidney, spleen, and intestine) in normal conditions relating to V. anguillarum infection. Many miRNAs were differentially regulated upon pathogen exposure. This work provides an opportunity for further understanding of the molecular mechanisms of miRNA regulation in C. semilaevis host-pathogen interactions.
authors.affiliation: Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China. Electronic address: shazx@ysfri.ac.cn.
authors.forename: Zhenxia
authors.initials: Z
authors.lastname: Sha
authors.affiliation: Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China.
authors.forename: Guangye
authors.initials: G
authors.lastname: Gong
authors.affiliation: Department of Psychiatry & Neurobiology Science, University of Virginia, VA 22911, USA.
authors.forename: Shaolin
authors.initials: S
authors.lastname: Wang
authors.affiliation: Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Tengzhou Fisheries Service Center, Tengzhou 277500, PR China.
authors.forename: Qilong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China. Electronic address: chensl@ysfri.ac.cn.
authors.forename: Songlin
authors.initials: S
authors.lastname: Chen
mesh_terms: D000818:Animals; D058070:Asymptomatic Diseases; D019295:Computational Biology; D005399:Fishes / Q000276:immunology; D015723:Gene Library; D060226:Head Kidney / Q000276:immunology*; D059014:High-Throughput Nucleotide Sequencing; D007107:Immune System; D007109:Immunity / Q000235:genetics; D008099:Liver / Q000276:immunology*; D035683:MicroRNAs / Q000235:genetics; D013154:Spleen / Q000276:immunology*; D014733:Vibrio / Q000276:immunology*; D014735:Vibrio Infections / Q000276:immunology*
chemical_list: D035683:MicroRNAs
keywords: Cynoglossus semilaevis; High-throughput sequencing; Immune; Vibrio anguillarum; miRNA