Phylogenetic Origin and Diversification of RNAi Pathway Genes in Insects

Abstract

RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders. We inferred the phylogenetic origin of insect-specific RNAi pathway genes and also identified several hitherto unrecorded gene expansions using whole-body transcriptome data from the international 1KITE (1000 Insect Transcriptome Evolution) project as well as other resources such as i5K (5000 Insect Genome Project). Specifically, we traced the origin of the double stranded RNA binding protein R2D2 to the last common ancestor of winged insects (Pterygota), the loss of Sid-1/Tag-130 orthologs in Antliophora (fleas, flies and relatives, and scorpionflies in a broad sense), and confirm previous evidence for the splitting of the Argonaute proteins Aubergine and Piwi in Brachyceran flies (Diptera, Brachycera). Our study offers new reference points for future experimental research on RNAi-related pathway genes in insects.

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

“…piRNAs are associated with PIWI-family Argonautes, which have undergone similar duplications. Piwi has duplicated in L. migratoria , the centipede Strigamia maritima , the pea aphid Acyrthosiphon pisum 18 , the mosquito Aedes aegypti 24 , and flies (generating piwi and aubergine 19 ). All species harbour a single copy of ago3 , which encodes the other PIWI-family Argonaute associated with piRNAs, except for A. pisum which has two ago3 genes.…”

“…Expansion and loss of key genes in the piRNA pathway has occurred in platyhelminths 16 , nematodes 17 , and arthropods 18–20 . This gene turnover is accompanied by a wide variety of functions for piRNAs, such as sex determination in the silkworm Bombyx mori and epigenetic memory formation in the nematode C. elegans 21 .…”

Molecular mechanisms influencing efficiency of RNA interference in insects

“…The A. mellifera Sil is upregulated in response to dsRNA, yet radiolabeled dsRNA is not taken up by any tissue except the fat body, supporting the idea that Sil proteins may not be involved in dsRNA uptake in Hymenoptera (Table S5). Intriguingly, insect Sil genes appear to be more closely related to the cholesterol uptake‐associated gene of C. elegans than to Sid1 , indicating that Sil genes serve different functions in insects and nematodes. Therefore, we are only able to conclude that Sils may participate in RNAi, at least in some insects, but the importance of this uptake mechanism is still unknown.…”

“…The small‐interfering RNA (siRNA) pathway (Fig. A), which is the main focus of this review, is naturally involved in defense against dsRNA of viral origin (exo‐siRNA) as well as in defense against transposable elements in the genome (endo‐siRNA) . The core enzymes of the siRNA pathway (e.g., Ago2, Dcr2, RISC) are present in all plants, animals, and fungi.…”

“…Extra copies of Ago2 and R2D2 are suspected to be responsible for the superior RNAi efficiency exhibited by T. castaneum compared with D. melanogaster , which only has a single copy of each core siRNA enzyme (Table S6). In addition, missing core enzyme genes are proposed to contribute to low RNAi efficiency in other species . However, genes encoding core enzymes for all three RNAi pathways have now been identified in a variety of species from every insect order (Table S6) and enzyme copy number does not clearly explain RNAi efficiency differences among insects.…”