Comparative analysis of dsRNA‐induced lncRNAs in three kinds of insect species

Abstract

Long noncoding RNAs (lncRNAs) that have immune responses to various stimuli have been identified in some insects. One type of pathogen-associated molecular pattern, double-stranded RNA (dsRNA), can trigger the RNA interference (RNAi) pathway and immune response. Interestingly, there has been no research into characterizing the relationship between lncRNA and dsRNA-induced RNAi pathways.In this study, dsRNA-induced lncRNAs were investigated in two species of lepidopteran insects, Helicoverpa armigera and Plutella xylostella, and one species of coleopteran insects, Tribolium castaneum. Between untreated group and dsRNAinduced group; 3,463 H. armigera, 6,245 P. xylostella, and 3,067 T. castaneum differentially expressed lncRNAs were identified while 156 H. armigera, 247 P. xylostella, 415 T. castaneum lncRNAs and their putative target genes showed consistent changes in gene expression. In T. castaneum, most target genes of the differentially expressed lncRNAs are enriched in the cyclic adenosine monophosphate signaling pathway, ABC transporters, and Janus kinase-signal transducers and activators of the transcription signaling pathway.Conversely, in H. armigera and P. xylostella, the differentially expressed lncRNAs were mainly enriched in the metabolic, digestive, and synthetic signaling pathways. This result indicates that dsRNA-induced lncRNA is species-dependent.We also found that both Dicer-2 and the lncRNA that targets Dicer-2 were significantly upregulated after dsRNA treatment in P. xylostella, indicating that some lncRNAs may be involved in the regulation of the core RNAi pathway in insects. Our results are the first to identify a relationship between lncRNAs and dsRNA in various insect species with different RNAi efficiencies. These results provide a reference for future study of the dsRNA-induced RNAi pathway and different RNAi efficiencies among insect species.

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

“…Additionally, Guan et al . obtained 2865 lncRNAs from 5th instar larvae of T. castaneum by CPC, txCdsPredict, CNCI and pfam (Guan et al ., 2020). With these four methods for coding capacity prediction, we identified a total of 4516 lncRNAs corresponding to 3917 loci from embryos, larvae, pupae and adults of T. castaneum .…”

“…Compared with protein‐coding genes, lncRNA genes are shorter and tend to have fewer exons and transcripts (Fig. 2) (Ali & Abd El Halim, 2020; Guan et al ., 2020). These features were also found in the lncRNAs of D. melanogaster (Chen et al ., 2016), B. mori (Wu et al ., 2016), A. mellifera (Liu et al ., 2019) and S. furcifera (Chang et al ., 2020).…”

“…Using CPC, CPAT and pfam for coding capacity analyses, 10 120 lncRNAs from 188 public RNA-seq datasets of eggs, larvae, pupae and adults in T. castaneum were found (Ali & Abd El Halim, 2020), but this amount is much greater than those in the majority of insects, including D. melanogaster (dos Santos et al, 2015;Chen et al, 2016), A. gambiae (Jenkins et al, 2015), A. aegypti (Etebari et al, 2016), A. cerana, A. mellifera (Jayakodi et al, 2015), P. xylostella (Etebari et al, 2015) and S. furcifera (Chang et al, 2020). Additionally, Guan et al obtained 2865 lncRNAs from 5th instar larvae of T. castaneum by CPC, txCdsPredict, CNCI and pfam (Guan et al, 2020). With these four methods for coding capacity prediction, we identified a total of 4516 lncRNAs corresponding to 3917 loci from embryos, larvae, pupae and adults of T. castaneum.…”

“…From its genome sequence, 1154 unique micro RNAs (miRNAs) were obtained by sequencing eight developmental stages (Wu et al ., 2017). Recent studies have identified a number of lncRNAs related to immune response (Ali & Abd El Halim, 2020) and double‐stranded RNA (dsRNA)‐induced RNA interference (RNAi) pathway in T. castaneum (Guan et al ., 2020), but it is still unclear how many lncRNAs there are in this insect and what their expression profiles are at different developmental stages. By contrast, high efficiency of RNAi was reported in T. castaneum (Tomoyasu & Denell, 2004; Tomoyasu et al ., 2008), and this advantage will promote a functional analysis of lncRNAs in this species.…”

There and Back Again: Hox Clusters Use Both DNA Strands

“…The increasing interest in lncRNAs raised the number of studies in which different insects, including those that did not belong to the classical models of molecular and genetic research, were used [ 50 , 83 , 153 , 154 , 155 , 156 , 157 ]. From these studies, it has emerged that insects possess lesser amounts than vertebrates but still significant repertoires of these molecules (from 2949 for Anopheles gambiae to 11,810 for Bombyx mori ).…”