Genome-wide analysis of long noncoding RNAs and their association in regulating the metamorphosis of the Sarcophaga peregrina (Diptera: Sarcophagidae).

Background: The flesh fly, Sarcophaga peregrina (Diptera: Sarcophagidae), is an important hygiene pest, that causes myiasis in humans and other mammals, typically livestock, and as a vector for various parasitic agents, including bacteria, viruses, and parasites. The role of long non-coding RNAs (lncRNAs) in regulating gene expression during metamorphosis of the flesh fly has not been well established. Methodology/Principal findings: In this study, we performed genome-wide identification and characterization of lncRNAs from the early pupal stage (1-days pupae), mid-term pupal stage (5-days pupae), and late pupal stage (9-days pupae) of S. peregrina by RNA-seq, and a total of 6921 lncRNAs transcripts were identified. RT-qPCR and enrichment analyses revealed the differentially expressed lncRNAs (DE lncRNAs) that might be associated with insect metamorphosis development. Furthermore, functional analysis revealed that the DE lncRNA (SP_lnc5000) could potentially be involved in regulating the metamorphosis of S. peregrina. RNA interference of SP_lnc5000 caused reduced expression of metamorphosis-related genes in 20-hydroxyecdysone (20E) signaling (Br-c, Ftz-F1), cuticle tanning pathway (TH, DOPA), and chitin related pathway (Cht5). Injection of dsSP_lnc5000 in 3rd instar larvae of S. peregrina resulted in deformed pupae, stagnation of pupal-adult metamorphosis, and a decrease in development time of pupal, pupariation rates and eclosion rates. Hematoxylin-eosin staining (H&E), scanning electron microscope (SEM) observation and cuticle hydrocarbons (CHCs) analysis indicated that SP_lnc5000 had crucial roles in the metamorphosis developmental by modulating pupal cuticular development. Conclusions/Significance: We established that the lncRNA SP_lnc5000 potentially regulates the metamorphosis of S. peregrina by putatively affecting the structure and composition of the pupal cuticle. This study enhances our understanding of lncRNAs as regulators of metamorphosis in S. peregrina, and provide valuable insights into the identification of potential targets for vector control and the development of effective strategies for controlling the spread of myiasis and parasitic diseases. Author summary: Sarcophaga peregrina, a significant flesh fly species, is closely associated with human life in its ecological habits, as vectors of parasitic disease agents, they can cause myiasis and other tropical infectious diseases, and has been implicated in the transmission of diseases such as cutaneous leishmaniasis. Enhance the understanding of metamorphosis of this species, have a significance for vector control. The lncRNAs plays important roles in growth development of insect. However, its role in regulating the metamorphosis of S. peregrina has not been reported so far. In this study, we obtained genome-wide identification of lncRNA profiles from different pupae developmental stages of S. peregrina. Furthermore, we performed a functional analysis of differentially expressed lncRNAs (SP_lnc5000) in regulating the metamorphosis of S. peregrina by RNA interference, and H&E staining, SEM observation and CHCs detection. The results provided here increase the knowledge on metamorphosis processes in S. peregrina, which is important for the design of new vector control strategies. [ABSTRACT FROM AUTHOR]