Xianhui Ning1,2,3,4, Li Sun5,6. 1. CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 266071, Qingdao, China. 2. College of Marine Science and Engineering, Nanjing Normal University, 210023, Nanjing, Jiangsu, China. 3. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. 4. Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, 222005, Lianyungang, Jiangsu, China. 5. CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 266071, Qingdao, China. lsun@qdio.ac.cn. 6. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. lsun@qdio.ac.cn.
Abstract
BACKGROUND: Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. RESULTS: Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. CONCLUSIONS: This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.
BACKGROUND: Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. RESULTS: Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. CONCLUSIONS: This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.
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