Interaction Analysis of lncRNA and mRNA Based on the Full-Length Transcriptome of the Nymph-to-Adult Developmental Transition of Sogatella furcifera

SIMPLE SUMMARY: Long noncoding RNAs (lncRNAs) have been reported to be involved in multiple biological processes. However, how lncRNA and mRNA cooperatively participate in regulating the molting process remains unknown. In this study, we constructed the full-length transcriptome of the nymph-to-adult developmental transition of Sogatella furcifera (white-backed planthopper) and identified three key lncRNAs: MSTRG.16086.1, MSTRG.16087.1, and MSTRG.2447.1, which may be involved in specific molting process of S. furcifera. Our results revealed that lncRNA may play a potential regulatory role and provide data for supporting further research on the molecular mechanism by which lncRNA and target genes regulate the molting of S. furcifera. ABSTRACT: Little is known on how long noncoding RNAs (lncRNAs) and mRNAs cooperatively participate in regulating the nymph-to-adult development transition of Sogatella furcifera. Herein, lncRNA and mRNA libraries were constructed in three different developmental stages of S. furcifera, namely, prior to (PE), during (DE), and after (AE) ecdysis. Overall, 4649 lncRNAs were identified and divided into intergenic (53.90%), intronic (1.33%), sense (8.99%), antisense (21.75%), and bidirectional (3.94%) lncRNAs. Moreover, 795 differentially expressed lncRNAs were identified. Specifically, upon comparing PE and DE, 2719 target mRNAs were predicted for 574 lncRNAs. Upon comparing PE and AE, 2816 target mRNAs were predicted for 627 lncRNAs. Finally, upon comparing DE and AE, 51 target mRNAs were predicted for 35 lncRNAs. Kyoto Encyclopedia of Genes and Genome functional enrichment analysis revealed that the target genes of 795 lncRNAs were enriched in metabolic pathways, amino sugar and nucleotide sugar metabolism, and fatty acid metabolism. Subsequently, interaction analysis indicated that MSTRG.16086.1, MSTRG.16087.1, and MSTRG.2447.1 were functionally associated with cuticle protein and chitin biosynthesis. Finally, 11 differentially expressed lncRNAs were significantly enriched in 3rd and 4th instar nymphs. Our findings suggest that lncRNAs play a critical regulatory role during the molting of S. furcifera.