Genome-wide identification and characterization of long non-coding RNAs inTribolium castaneum

Long non-coding RNAs (lncRNAs) are poorly understood in insects. In this study, we performed genome-wide analysis of lncRNAs inTribolium castaneumby RNA-seq. In total, 4516 lncRNA transcripts corresponding to 3917 genes were identified from late embryos, early larvae, late larvae, early pupae, late pupae and early adults ofT. castaneum, including 3152 novel lncRNAs and 1364 known lncRNAs. These lncRNAs have few exons and transcripts, and are short in length. During development, they exhibited nine different expression patterns. Functionally, they can act either by targeting messenger RNAs (1813 lncRNAs) and lncRNAs (45 lncRNAs) or as micro RNA (miRNA) precursors (46 lncRNAs). LncRNAs were observed to target the metabolic enzymes of glycolysis, TCA cycle and amino acids, demonstrating that lncRNAs control metabolism by regulating metabolic enzymes. Moreover, lncRNAs were shown to participate in cell differentiation and development via their targets. As miRNA precursors, lncRNAs could participate in the ecdysone signaling pathway. This study provides comprehensive information for lncRNAs ofT. castaneum, and will promote functional analysis and target identification of lncRNAs in the insect.

Automated summary

This study conducted a genome-wide analysis of lncRNAs in Tribolium castaneum through RNA-seq, identifying numerous novel lncRNAs and examining their diverse expression patterns during insect development. Functionally, lncRNAs were found to regulate metabolic enzymes, cell differentiation, and participate in the ecdysone signaling pathway by targeting mRNAs, lncRNAs, or serving as miRNA precursors.