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Applied Biochemistry and Biotechnology

, Volume 179, Issue 8, pp 1393–1403 | Cite as

Insilco Prediction and Characterization of microRNAs from Oncopeltus fasciatus (Hemiptera: Lygaeidae) Genome

  • R. EllangoEmail author
  • R. AsokanEmail author
  • V. V. Ramamurthy
Article

Abstract

For studies on functional genomics, small RNAs, especially microRNAs (miRNAs), have emerged as a hot topic due to their importance in cellular and developmental processes. Identification of insect miRNAs largely depends on the availability of genomic sequences in the public domain. The large milkweed bug, Oncopeltus fasciatus (Dallas) is a hemimetabolous insect which has become a model hemipteran system for various molecular studies. In this study, we identified 96 candidate mature miRNAs from O. fasciatus genome using a blast search with the previously reported animal miRNAs. The secondary structure of predicted miRNA sequences was determined online using “mfold” web server and verified by calculating the minimal free energy index (MFEI). Six miRNAs let-7e, miR-133c, miR-219b, mir-466d, mir-669f, and mir-669l are reported for the first time in Insecta. Comparison of O. fasciatus mir-2 and mir-71 family clusters to those of diverse insect species showed that they are highly conserved. The phylogenetic analysis of miRNAs revealed the evolutionary relationship of conserved miRNAs of O. fasciatus with other insect species. Using a classical rule-based algorithm method, we predicted the possible targets of the new miRNAs. Our study not only identified the list of miRNAs in O. fasciatus but also provides a basic platform for developing novel pest management strategies based on artificial miRNAs.

Keywords

O. fasciatus miRNA Insect genome MFEI value Target prediction 

Notes

Acknowledgments

Our sincere thanks are due to the Director, Indian Institute of Horticultural Research, Bengaluru, India, for providing the facilities and encouragement. We gratefully acknowledge the financial support received from the Indian Council of Agricultural Research (ICAR), New Delhi through the XIIth plan Network Project on ORP-on Management of sucking pest on horticultural crops.

Supplementary material

12010_2016_2072_MOESM1_ESM.xls (47 kb)
Table S1 Oncopeltus fasciatus mature miRNA details. (XLS 47 kb)
12010_2016_2072_MOESM2_ESM.xls (39 kb)
Table S2 O. fasciatus precursor miRNA details. (XLS 39 kb)
12010_2016_2072_MOESM3_ESM.xls (32 kb)
Table S3 Prediction of possible targets of O. fasciatus miRNA. (XLS 32 kb)
12010_2016_2072_MOESM4_ESM.xls (76 kb)
Table S4 Both Miranda and RNA hybrid were used to predict the possible target for six ofa-miRNAs. (XLS 75 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Division of BiotechnologyIndian Institute of Horticultural Research (IIHR)BangaloreIndia
  2. 2.Division of EntomologyIndian Agricultural Research Institute (IARI)Pusa CampusIndia

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