Transcriptome analysis demonstrate widespread differential expression of long noncoding RNAs involve in Larimichthys crocea immune response

Long noncoding RNAs (IncRNAs) are a class of transcripts that longer than 200 bp and do not encode proteins. Recent genome-wide studies of vertebrate transcriptomes have annotated IncRNAs 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 IncRNAs in this species. In order to obtain a catalog of IncRNAs 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 IncRNAs were specifically enriched in different tissues. A stringent set of 210 IncRNAs were identified as being specifically expressed in spleen and potentially involved in immune response. Our study first systematically identify IncRNAs in large yellow croaker, benefiting the future genomic study of this species. (C) 2016 Elsevier Ltd. All rights reserved.