Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection

Abstract

Aedes albopictus (Ae. albopictus) is an important vector of arboviruses such as Dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV). Long noncoding RNA (lncRNAs) have been identified in other vectors including Aedes aegypti and Anopheles mosquitoes, few of which have been implicated in immunity and viral replication. To identify lncRNAs with potential biological functions in Ae. albopictus, we performed RNA-seq on Ae. albopictus cells infected with DENV and ZIKV, and analyzed them together with public datasets. We identified a total of 23,899 transcripts, 16,089 were intergenic while 3,126 and 4,183 of them were antisense and intronic to annotated genes respectively. Ae. albopictus lncRNAs shared many of the characteristics with their invertebrate and vertebrate counterparts, such as low expression, low GC content, short in length, and low conservation even among closely related species. Compared to protein-coding genes, lncRNAs exhibited higher tendency to be expressed in a stage-specific manner. Besides, expression of lncRNAs and nearest protein-coding genes tended to be correlated, especially for the gene pairs within 1kb from each other. We also discovered that Ae. albopictus lncRNAs have the potential to act as precursors for miRNA and piRNAs, both of which have been implicated in antiviral defense in Aedes mosquito. Upon flavivirus infection, lncRNAs were observed to be differentially expressed, which possibly indicates the involvement of lncRNAs in the host-antiviral defense. Our study provides the first systematic identification of lncRNAs in Ae. albopictus, hence, offering a foundation for future studies of lncRNA functions.