siRNAs and piRNAs collaborate for transposon control in the two-spotted spider mite

Abstract

RNAi has revolutionized genetic research, and is being commercialized as an insect pest control technology. Mechanisms exploited for this purpose are antiviral and therefore rapidly evolving. Ideally RNAi will also be used for noninsect pests; however, differences in RNAi biology make this uncertain. (two-spotted spider mite) is a destructive noninsect pest, which has a proclivity to develop pesticide resistance. Here we provide a comprehensive study of the endogenous RNAi pathways of spider mites to inform design of exogenous RNAi triggers. This effort revealed unexpected roles for small RNAs and novel genome surveillance pathways. Spider mites have an expanded RNAi machinery relative to insects, encoding RNA dependent RNA polymerase (Rdrp) and extra Piwi-class effectors. Through analyzing transcriptome data we explored small RNA biogenesis, and discovered five siRNA loci that appear central to genome surveillance. These RNAs are expressed in the gonad, which we hypothesize to trigger production of piRNAs for control of transposable elements (TEs). This work highlights the need to investigate endogenous RNAi biology as lessons from model organisms may not hold in other species, impacting development of an RNAi strategy.

Environmental RNAi pathways in the two-spotted spider mite

“…A potential benefit of distinct miRNA/siRNA pathways could be to allow rapid evolution of siRNA behavior for antiviral or genome defense, something that is incongruent with conservation of miRNA function [ 5 ]. Organisms distant from Drosophila show distinct small RNA biology, which is most apparent in chelicerates such as the two-spotted spider mite, Tetranychus urticae , the subject of this study [ 6 – 8 ]. Hundreds of different crops and ornamental plants are infested by spider mites.…”

Assessing Environmental RNAi in a Non-Model Organism

“…This is highly suggestive of piRNAs, which exhibit these features as a result of piRNA "ping-pong" processing 20 . In spider mites siRNAs and piRNAs cooperate for genome surveillance 15 . These results suggest this may extend to siRNAs derived from exogenous sources, which likewise appear to be able to trigger piRNA production.…”

“…A python-based algorithm was used to find overlapping read pairs that represent Dicer cleavage produced small RNA duplexes 37 . Small RNAs of [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] nts were used to query target pairs, also 15-31 nts long, that exhibited an overlap of 2 nts less than the size of query RNA. The number of reads for each pair was plotted to show a heatmap matrix.…”

“…Thus, this approach may also reveal a Rdrp signature for this group. Additionally, spider mites unlike D. melanogaster have a central role for siRNAs in genome surveillance 15,16 .…”

Potential Role of Accessory Domains in Polyproteins Encoded by Retrotransposons in Anti-viral Defense of Host Cells

“…We proposed hypothetic evolutionary scenarios explaining the natural selection-supported preservation of the retrotransposon SF1H domains in insect genomes and considered two basic alternatives to explain the long-term evolutionary fixation of SF1 HEL in retrotransposons, namely, significance of this genetic element as advantageous for (i) transposons themselves or (ii) their insect hosts (Morozov et al, 2017). In one scenario, we supposed that both siRNA- and piRNA-mediated pathways blocking expression and transposition of retroelements (Ito, 2012; Lazareva et al, 2015; Guida et al, 2016; Mondal et al, 2018) can be suppressed by the encoded SF1H silencing suppressor activity. Also SF1H-coding sequences acquired by retrotransposons might be adapted for direct co-operative work with reverse-transcribing enzymes to improve efficiency of cDNA synthesis and transposition of these selfish genetic elements (Morozov et al, 2017).…”