Revised annotation and characterization of novelAedes albopictusmiRNAs and their potential functions in dengue virus infection

Abstract

The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is a highly invasive species that transmit several arboviruses including dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV).Although several studies have identified microRNAs (miRNAs) in Ae. albopictus, it is crucial to extend and improve current annotations with the newly improved genome assembly, and the increase number of small RNA-sequencing data. We combined our high-depth sequence data and 26 public datasets to re-annotate Ae. albopictus miRNAs, and found a total of 110 novel mature miRNAs. We discovered that the expression of novel miRNAs was lower than known miRNAs. Furthermore, compared to known miRNAs, novel miRNAs are prone to be expressed in stage-specific manner. Upon DENV infection, a total of 59 novel miRNAs were differentially expressed, and target prediction analysis revealed that miRNA-target genes were involved in lipid metabolism and protein processing in endoplasmic reticulum. Taken together, miRNA annotation profile provided here is the most comprehensive to date, and we believed that this will facilitate future research in understanding virushost interactions particularly on the role of miRNAs. during virus infection, and at diapause condition (Avila-Bonilla et al., 2017;Batz et al., 2017;Liu et al., 2015;Su et al., 2019Su et al., , 2017. These studies suggest the involvement of miRNAs in the regulation of Ae. albopictus development and virus infection.High quality genome coupled with high-depth RNA-sequencing data are important for accurate and comprehensive annotation of coding and non-coding genes. Alignment of small RNA reads to the reference genome is an essential step to annotate miRNAs in a species. Several studies used genome of closely related species as proxy reference to facilitate the miRNA expression analysis (Etebari et al.,