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Open Access Highly Accessed Research article

Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor

Chitvan Khajuria17, Christie E Williams2, Mustapha El Bouhssini3, R Jeff Whitworth1, Stephen Richards4, Jeffrey J Stuart5 and Ming-Shun Chen167*

Author Affiliations

1 Department of Entomology, Kansas State University, Manhattan, Kansas, 66056, USA

2 USDA-ARS and Department of Entomology, Purdue University, West Lafayette, IN, 47097, USA

3 International Center for Agricultural Research in the Dry Area, Aleppo, Syria

4 Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA

5 Department of Entomology, Purdue University, West Lafayette, IN, 47097, USA

6 Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton, Kansas State University, Manhattan, KS, 66506, USA

7 Current Address: Department of Entomology, University of Nebraska, Lincoln, NE, 68583, USA

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BMC Genomics 2013, 14:187  doi:10.1186/1471-2164-14-187

Published: 18 March 2013

Abstract

Background

MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a destructive pest of wheat and model organism for studying gall midge biology and insect – host plant interactions.

Results

In this study, we systematically analyzed miRNAs from the Hessian fly. Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species. A genome-wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Analysis of the 611 putative genes revealed a striking feature: the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes.

Conclusion

The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior. The dramatic expansion of identical or similar miRNAs provides a unique system to study functional relations among miRNA iso-genes as well as changes in sequence specificity due to small changes in miRNAs and in their mRNA targets. These results may also facilitate the identification of miRNA genes for potential pest control through transgenic approaches.