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      Comparative analysis of double-stranded RNA degradation and processing in insects

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          Abstract

          RNA interference (RNAi) based methods are being developed for pest management. A few products for control of coleopteran pests are expected to be commercialized soon. However, variability in RNAi efficiency among insects is preventing the widespread use of this technology. In this study, we conducted research to identify reasons for variability in RNAi efficiency among thirty-seven (37) insects belonging to five orders. Studies on double-stranded RNA (dsRNA) degradation by dsRNases and processing of labeled dsRNA to siRNA showed that both dsRNA degradation and processing are variable among insects belonging to different orders as well as among different insect species within the same order. We identified homologs of key RNAi genes in the genomes of some of these insects and studied their domain architecture. These data suggest that dsRNA digestion by dsRNases and its processing to siRNAs in the cells are among the major factors contributing to differential RNAi efficiency reported among insects.

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          Most cited references58

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          NIH Image to ImageJ: 25 years of image analysis.

          Lynda C. Schneider, Wayne S Rasband (2013)
          For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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            The Pfam protein families database.

            A. Bateman, Lachlan Coin (2004)
            Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
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              SMART: recent updates, new developments and status in 2015

              Ivica Letunic, Tobias Doerks, Peer Bork (2014)
              SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's ‘Genomic’ mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine.
              Article 0 comments Cited 638 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Subba Reddy Palli: rpalli@email.uky.edu
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 6 December 2017
                Publication date PMC-release: 6 December 2017
                Publication date Collection: 2017
                Volume: 7
                Electronic Location Identifier: 17059
                Affiliations
                [1 ]ISNI 0000 0004 1936 8438, GRID grid.266539.d, Department of Entomology, College of Agriculture, Food and Environment, Agriculture Science Center North, University of Kentucky, ; Lexington, KY USA
                [2 ]ISNI 0000 0001 2109 4999, GRID grid.8195.5, Present Address: Molecular Biology Research Lab., Department of Zoology, Deshbandhu College, University of Delhi, ; New Delhi, India
                [3 ]ISNI 0000 0001 2176 2352, GRID grid.412577.2, Present Address: Punjab Agricultural University, Regional Station, ; Faridkot, Punjab India
                [4 ]ISNI 0000 0004 1764 745X, GRID grid.462331.1, Present Address: Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, ; Ajmer, Rajasthan India
                Article
                Publisher ID: 17134
                DOI: 10.1038/s41598-017-17134-2
                PMC ID: 5719073
                PubMed ID: 29213068
                SO-VID: aee9085b-1279-4866-bcf6-b2be14ab84c6
                Copyright © © The Author(s) 2017
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 27 June 2017
                Date accepted : 24 October 2017
                Categories
                Subject: Article
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                issue-copyright-statement © The Author(s) 2017

                ScienceOpen disciplines: Uncategorized
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