MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi

Abstract

MicroRNAs (miRNAs) are endogenous, single-stranded small RNAs that have important regulatory functions at the post-transcriptional level. Here, we characterize miRNAs in two divergent mosquito species, Aedes aegypti and Anopheles stephensi, through deep sequencing of small RNAs spanning all developmental stages. We discovered eight novel miRNAs in Ae. aegypti and 20 novel miRNAs in An. stephensi, which enabled the first systematic analysis of miRNA evolution in mosquitos. We traced the phylogenetic history of all miRNAs in both species and report a rate of 0.055–0.13 miRNA net gain per million years. Most novel miRNAs originate de novo. Duplications that produced miRNA clusters and families are more common in Ae. aegypti than in An. stephensi. We also identified arm-switch as a source of new miRNAs. Expression profile analysis identified mosquito-specific miRNAs that showed strong stage-specific expression in one or both lineages. For example, the aae-miR-2941/2946 family represents the most abundant maternally-deposited and zygotically transcribed miRNAs in Ae. aegypti. miR-2943 is a highly expressed zygotic miRNA in both Ae. aegypti and An. stephensi. Such information provides the basis to study the function of these miRNAs in biology common to all mosquitos or unique to one particular lineage.

Mosquito-specific microRNA-1890 targets the juvenile hormone-regulated serine protease JHA15 in the female mosquito gut

“…9,10,[28][29][30][31][32] Phenotypic divergence among animal species may be due in part to lineage-and species-specific regulation of gene expression by miRNAs. miRNAs restricted to mosquitoes may contribute to mosquito-specific functions and, as such, have potential for contributing to the development of novel mosquito control approaches.…”

MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum

“…Previous studies by us and others have shown that members of one of these clusters (mir-309 6) in Drosophila are strongly up-regulated in the early fly blastoderm (Biemar et al 2005;Ninova et al 2014), and that members of the homologous clusters in A. mellifera (mir-3478 318) and mosquitoes (mir-309 286) are also highly expressed in early embryos (Zondag et al 2012;Hu et al 2014). In addition, the mosquito-specific mir-2941 2946 cluster, whose 3 ′ mature sequences have the same seed as miR-3889-3p in T. castaneum, are the most abundant microRNAs in the early stages of development (Hu et al 2014). We detect nascent primary transcripts of mir-9d 3791 and mir-3889 3843 in the early blastoderm nuclei of T. castaneum by in situ hybridization (Supplemental Fig.…”

“…5C); clusters encoding homologs of the conserved mir-9, mir-2944, mir-279, mir-3791, and mir-309 families are found in other insect lineages and represent one of the most extreme examples of microRNA gain, loss, duplication, and rearrangement reported to date (Ninova et al 2014). Previous studies by us and others have shown that members of one of these clusters (mir-309 6) in Drosophila are strongly up-regulated in the early fly blastoderm (Biemar et al 2005;Ninova et al 2014), and that members of the homologous clusters in A. mellifera (mir-3478 318) and mosquitoes (mir-309 286) are also highly expressed in early embryos (Zondag et al 2012;Hu et al 2014). In addition, the mosquito-specific mir-2941 2946 cluster, whose 3 ′ mature sequences have the same seed as miR-3889-3p in T. castaneum, are the most abundant microRNAs in the early stages of development (Hu et al 2014).…”

MicroRNA evolution provides new evidence for a close relationship of Diplura to Insecta

“…In insects, the changes to the cluster were complex, with more new additions, although Mir-9 and Mir-2944 remained in the cluster and duplicated in higher insects. This cluster has been found to be highly expressed in early embryos of flies, bees, mosquitoes and beetles (Zondag et al, 2012;Hu et al, 2014;Ninova et al, 2014;Ninova et al, 2016). Its highly varied composition and functional evolution deserve special attention and in-depth research.…”