title: Transcriptome analysis demonstrate widespread differential expression of long noncoding RNAs involve in Larimichthys crocea immune response.
abstract: Long noncoding RNAs (lncRNAs) are a class of transcripts that longer than 200 bp and do not encode proteins. Recent genome-wide studies of vertebrate transcriptomes have annotated lncRNAs that are expressed in various tissues and development stages. The draft genome and several transcriptome sequencing data sets have been collected for the study of protein-coding genes in large yellow croaker (Larimichthys crocea), but little is known about the expression and functional roles of lncRNAs in this species. In order to obtain a catalog of lncRNAs for large yellow croaker, several RNA-seq datasets were integrated from various tissues including egg, muscle, liver, and spleen. A total of 48,953 high-confidence transcripts were reconstructed in 38,017 loci, recovering the most of expressed reference transcripts while thousands of novel expressed loci have been identified. The tissue expression profile revealed that most lncRNAs were specifically enriched in different tissues. A stringent set of 210 lncRNAs were identified as being specifically expressed in spleen and potentially involved in immune response. Our study first systematically identify lncRNAs in large yellow croaker, benefiting the future genomic study of this species.
authors.affiliation: National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Jiang
authors.affiliation: National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China.
authors.forename: Aiyi
authors.initials: A
authors.lastname: Zhu
authors.affiliation: National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China.
authors.forename: Jianshe
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Bsgenomics Co., Ltd., Shenzhen, China.
authors.forename: Jiajian
authors.initials: J
authors.lastname: Zhou
authors.affiliation: National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China. Electronic address: wucw2013@126.com.
authors.forename: Changwen
authors.initials: C
authors.lastname: Wu
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000662:veterinary; D007113:Immunity, Innate; D009928:Organ Specificity; D010473:Perciformes / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000662:veterinary; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding
keywords: Immune response; Larimichthys crocea; Long noncoding RNAs; RNA-seq