Computational identification and characterization of putative miRNAs in Heliothis virescens

Abstract

Heliothis virescens, a polyphagous pest, is one of the most destructive pests of many crops and vegetables. Various insecticides and pesticides are used by agriculturalists to stop the growth and development of this pest. RNA interference is a new area for the management of pests/insects by inhibiting the growth related RNAs. This involves the miRNAs identification and its characterization. In the present study, computational approach is applied to predict putative miRNA candidates along with their possible target(s) in the Heliothis virescens. A total of 63,662 ESTs were downloaded from dbEST database and processed, trimmed and masked through EGassembler. The H. virescens contigs database obtained after assembly was now used to find the putative miRNA candidates by performing a local BLAST with the miRNAs of insects retrieved from miRBase. We have predicted putative miRNA candidates by homology search against all the reported insect miRNAs. These putative miRNAs candidates were further validated and filtered by different features. In addition, we have also attempted to predict the putative targets of these filtered miRNAs, by making use of 3' untranslated regions of mRNAs from B. mori. These miRNAs and their targets in H. virescens will help in improved understanding of molecular mechanisms of miRNA and development of novel and more precise techniques for better understanding some post transcriptional gene silencing.

Genome-Wide Screening and Functional Analysis Reveal That the Specific microRNA nlu-miR-173 Regulates Molting by Targeting Ftz-F1 in Nilaparvata lugens

“…Benefiting from the high-throughput sequencing technology coupled with bioinformatic methods, increasing numbers of miRNAs have been identified many species of insects (Legeai et al, 2010; Liu et al, 2010; Wei et al, 2011; Chilana et al, 2013; Tan et al, 2014). Generally, there are hundreds of known miRNAs in any given insect species, such as Aedes aegypti, B. mori, D. melanogaster , and Tribolium castaneum with 124, 563, 466, and 430 known mature miRNAs, respectively, according to miRBase 21.0.…”

Development associated profiling of chitinase and microRNA of Helicoverpa armigera identified chitinase repressive microRNA

“…By sequencing small RNA libraries of M. sexta embryos, larvae, pupae and adults, 163 conserved and 13 novel miRNAs have been identified so far13. Homology-based predictions of lepidopteran miRNAs have been conducted in H. armigera and H. virescens 1415. Nevertheless, a few miRNAs that control metamorphic transition from larvae to pupae have been functionally identified in B. mori 16.…”

Computational Identification of Dengue Virus MicroRNA-Like Structures and Their Cellular Targets

“…Nevertheless, it is well known that in animal systems, miRNA targets are difficult to predict because miRNA and mRNA pairs frequently contain several mismatches, gaps, and G + U base pairs in many positions. 26 In this study, pairwise comparison of whole human 3′-UTRs against eight mature miRNA of DENV has been conducted. The miRanda algorithm was used, which incorporates thermodynamic stability calculations of miRNA:mRNA* duplexes and alignment procedures for detecting the probable binding site on the 3′-UTRs.…”

“…The parameters assigned for miRanda hybridization included a default alignment score ≥ 140 and an MFE for an miRNA:miRNA* duplex of ≤−35 kcal/mol, and the other parameters were kept as default. 26 The matched UTRs were submitted to the NCBI BLAST platform to visualize the genome context, and the biological function was annotated. The diverse steps involved in the identification and target prediction of the miRNAs from DENV are presented in Figure 1 .…”