Divergent RNAi Biology in Mites and Development of Pest Control Strategies

RNA interference (RNAi) has transformed genetics research by revolutionizing reverse genetics in the nearly three decades that have passed since its discovery. ~19-31 nt small non-coding RNAs play a central role in RNAi biology, and are found in all multicellular eukaryotes. In these animals, three major classes of small RNAs have been described: microRNA (miRNA), small interfering RNA (siRNA), and Piwi interacting RNA (piRNA), which are produced in distinct yet occasionally overlapping pathways. While miRNAs are involved in tuning endogenous gene expression, piRNAs and siRNAs are essential for defense against viruses and transposons. Argonaute proteins are the main effectors in RNAi biology; they associate with small RNAs forming RNA induced silencing complex (RISC), which finds target transcripts by complementary base-pairing between small RNA and target leading to destruction or inhibition of expression. In the present study, we sought to investigate the RNAi pathways in two basal arthropods; a major allergy causing agent—dust mites, and the most polyphagous and pesticide resistant plant pest—spider mites. We have discovered that the piRNA pathway is absent in dust mite, and has been integrated into a derived siRNA pathway in spider mites. The spider mite siRNA pathway, which appears to work upstream of piRNA biogenesis, is gonad specific, and is a complete reversal of worm’s piRNA biology. Besides a laboratory tool, RNAi is being developed into an efficient pest-control technique to knock down gene expression in a single, targeted species. In such strategy, RNAi is triggered by long double-stranded RNAs, which get incorporated into the endogenous RNAi machinery producing siRNA, and trigger cleavage of complementary target transcripts. So far, RNAi technology is largely unsuccessful against spider mites, and the present study will help to design effective RNAi technology in future. Moreover, many species have been found insensitive to RNAi such as lepidopterans and hemipterans. Barriers in gut biology inhibit successful RNAi in these animals, which can be prevented if dsRNAs being delivered to epithelial cells effectively. To address this, we have developed a cationic polymeric delivery vehicle in this study that was successful in fall armyworm, a traditionally RNAi recalcitrant insect pest

Deep Experimental Profiling of microRNA Diversity, Deployment, and Evolution Across the \u3ci\u3eDrosophila\u3c/i\u3e Genus

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution

Deep Experimental Profiling of MicroRNA Diversity, Deployment, and Evolution Across the \u3ci\u3eDrosphila\u3c/i\u3e Genus

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution

Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus.

In the above-mentioned article, one of the coauthor names was misspelled and has now been corrected online as Md Mosharrof Hossain Mondal