Abstract
BackgroundSmall RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector.ResultsWe performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3’UTR of protein coding genes. Unusually, many TEs and the 3’UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs.ConclusionsThis is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1257-2) contains supplementary material, which is available to authorized users.
Highlights
Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites
In the adult gonads of both sexes reads mapping to transposons dramatically increased relative to the larval conditions, concomitant with an increased average size of small RNA consistent with the known size distribution of Piwi interacting RNAs (piRNAs) in other organisms, suggesting that this class represents the majority of the small RNAs produced in these tissues (Figure 1E, F and G)
In this study we have greatly increased the known complement of small regulatory RNAs in the mosquito A. gambiae, identifying a large number of novel microRNAs, revealing the extent of endogenous small interfering RNAs (siRNAs) production and describing for the first time the presence of piRNAs with likely roles in transposon control in the germline and possibly roles in the control of a limited number of endogenous genes
Summary
Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. In recent years additional layers of complexity have been revealed in the regulation of gene expression following the discovery in animals of several classes of small RNA molecules that can act at both the transcriptional and post-transcriptional level. Many of these small RNAs themselves show tissue-specific expression and have been shown to be essential for correct organogenesis and developmental progression. The second clade contains the Piwi proteins, expressed in the germline, composed of AGO3, Piwi and Aubergine (Aub) that bind to Piwi interacting RNAs (piRNAs)
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