title: Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.
abstract: Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Chuang
authors.initials: C
authors.lastname: Mu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China. rjwang@ouc.edu.cn.
authors.forename: Ruijia
authors.initials: R
authors.lastname: Wang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Tianqi
authors.initials: T
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Yuqiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Meilin
authors.initials: M
authors.lastname: Tian
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Wenqian
authors.initials: W
authors.lastname: Jiao
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Xiaoting
authors.initials: X
authors.lastname: Huang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China. zmbao@ouc.edu.cn.
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D000818:Animals; D019295:Computational Biology; D005786:Gene Expression Regulation; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D047332:Holothuria / Q000187:drug effects / Q000235:genetics* / Q000276:immunology; D007113:Immunity, Innate; D008070:Lipopolysaccharides / Q000494:pharmacology; D035683:MicroRNAs / Q000235:genetics* / Q000276:immunology; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000276:immunology; D012333:RNA, Messenger / Q000235:genetics* / Q000276:immunology; D012038:Regeneration / Q000187:drug effects / Q000235:genetics* / Q000276:immunology; D017423:Sequence Analysis, RNA; D047528:Stichopus / Q000187:drug effects / Q000235:genetics* / Q000276:immunology; D051193:Toll-Like Receptors / Q000235:genetics / Q000276:immunology; D011503:Transglutaminases / Q000235:genetics / Q000276:immunology
chemical_list: D008070:Lipopolysaccharides; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D051193:Toll-Like Receptors; D011503:Transglutaminases; C105804:transglutaminase 1
keywords: Innate immune response; Long non-coding RNA (lncRNA); RNA-seq; Sea cucumber; Tissue regeneration