Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1

Dengue virus (DENV) is a single-stranded, positive-strand RNA virus that belongs to the family of Flaviviridae, and it is mainly transmitted by the mosquito Aedes aegypti (Ae. aegypti). Understanding the interaction of the virus with mosquito vector is vital for devising new strategies for preventing virus transmission. Although protein-coding genes have been the central focus, many reports indicated that long non-coding RNAs (lncRNAs) were also involved in virus-host interaction. Recently, the latest version of Ae. aegypti genome (AaegL5) was released, and the assembly was up to chromosome level. This prompted us to perform lncRNA identification and characterization using the latest genome release as reference. In this study, we investigated the transcriptome profiles of both protein-coding and lncRNA genes in Aedes aegypti cells upon DENV infection. By combining RNA-seq libraries generated in this study with publicly available datasets, we identified a total of 7,221 novel lncRNA transcripts, of which 3,052 and 3,620 were intronic and intergenic respectively, while 549 were antisense to the reference genes. A total of 2,435 differentially expressed transcripts, of which 956 of them were lncRNAs. Overall, the distribution of lncRNA expression and fold change upon virus infection were lower than that of protein-coding genes. We found that the expression of immune-related genes involved in IMD and MAPK signaling pathways were altered. In addition, the expression of major genes involved in RNA-interference (RNAi) pathway that confers antiviral resistance in mosquitoes were found to be unchanged upon DENV infection. Gene ontology analysis suggests that differentially expressed transcripts, either upregulated or downregulated, generally belong to the same functional categories or working in similar signaling pathways. Taken together, besides providing a new set of lncRNA repertoire, the outcomes of our study offer better understanding of Ae. aegypti responses to DENV infection at gene level. Author Summary Dengue virus (DENV), a single-stranded and positive-strand RNA virus of the family Flaviviridae, is primarily transmitted by Aedes aegypti (Ae. aegypti) mosquitoes. There are four closely related but antigenically different serotypes of dengue virus namely DENV1-4. Our understanding on the interaction of each serotype of DENV with its mosquito vector is still very limited. Since vector-borne viruses pose significant burden to public health, knowledge on the virus-host interaction at the molecular level is essential, especially in developing effective strategies to control virus transmission. In this study, we embarked on investigating the transcriptional response of long non-coding RNAs (lncRNAs) and protein-coding genes upon dengue virus serotype 1 (DENV1) infection. Besides, we also generate a comprehensive list of novel lncRNAs identified from the latest and improved genome version of Ae. aegypti. Similar to protein-coding genes, we discovered that the overall expression of lncRNA was significantly altered, suggesting that lncRNAs were involved in virus-host interaction. The results of this study provide basic understanding on the interaction between DENV1 and Ae. aegypti vector at the transcriptional level.