Genome‐wide identification and characterization of long non‐coding RNAs in Tribolium castaneum

Abstract

Long non-coding RNAs (lncRNAs) are poorly understood in insects. In this study, we performed genome-wide analysis of lncRNAs in Tribolium castaneum by RNAseq. 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 of T. 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 of T. castaneum, and will promote functional analysis and target identification of lncRNAs in the insect.

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

“…For example, lncRNAs were identified in different developmental stages of T. castaneum. These results suggested that lncRNAs could act on the metabolic enzymes related to development [9].…”

“…Molting is an important event in the development process of arthropods, which undergoes a series of physiological changes such as the forming and degradation of the cuticle, internal tissue apoptosis and remodeling, and other physiological processes [35]. lncRNA expression in the biological processes of development have been examined in insects [7,9]. In the mites, lncRNA has been identified in many physiological processes of mites such as V. destructor [33], T. cinnabarinus [34], and Dermatophagoides farina [36].…”

“…The lncRNAs are divided into four categories (sense, antisense, intronic, and intergenic) based on their position and direction of transcription about the protein-coding genes [5]. Sequencing technology has identified abundant lncRNAs in some species and verified lncRNAs to be important regulators of biological processes rather than simply transcription byproducts [6][7][8][9][10]. lncRNAs could regulate the expression of protein-coding genes by cis-regulation of near genes and trans-regulation of terminal 2 of 13 genes in multiple biological processes, such as mRNA transcription, post-transcription, and stability [11,12].…”

“…lncRNAs have been identified in Sogatella frucifera [8], Tribolium castaneum [9], Drosophila melanogaster [13], Locusta migratoria [14], Apis cerana [15], Plutella xylostella [16], and Bombyx mori [17]. The functional annotation of lncRNAs in insect species has revealed that they can regulate immunity, behavioral plasticity, development, fecundity, and resistance [18][19][20][21][22].…”

Long Non-Coding RNAs in Insects

“…Even though lncRNAs have been discovered from many insect species, most of our knowledge about the functional aspect of insect lncRNAs comes from studies in Drosophila melanogaster . Besides Drosophila , lncRNAs have also been reported in Anopheles gambiae [ 19 ], Apis mellifera [ 20 ], Bombyx mori [ 21 ], and Tribolium castaneum [ 22 , 23 ]. With the advent of next-generation sequencing (NGS) technologies, large numbers of lncRNAs have been identified, but most of them remain functionallyunvalidated [ 24 ].…”