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

item KHAJURIA, CHITVAN - Kansas State University
item Williams, Christie
item BOHSSINI, MUSTAFA EL - International Center For Agricultural Research In The Dry Areas (ICARDA)
item WHITWORTH, JEFF - Kansas State University
item RICHARDS, STEPHEN - Baylor University
item STUART, JEFFREY - Purdue University
item Chen, Ming-Shun

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/11/2013
Publication Date: 3/18/2013
Publication URL:
Citation: Khajuria, C., Williams, C.E., Bohssini, M., Whitworth, J.R., Richards, S., Stuart, J.J., Chen, M. 2013. Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor. Biomed Central (BMC) Genomics. 14:187.

Interpretive Summary: Hessian fly is a destructive pest of wheat. The insect is mainly controlled through host plant resistance, but resistance genes in wheat are usually overcome within a few years by new fly biotypes. Alternative control measures are needed for effective management of the Hessian fly. Rapid advances in genomics and biotechnology bring new approaches for pest control. One of the promising new means for insect control is based on small, non-coding RNAs: small interfering RNAs (siRNAs) and microRNAs (miRNAs). Small RNAs can silence insect genes, resulting in the death of the insect. This study identified and characterized miRNAs and their genes systematically for the first time in Hessian fly. A large number of miRNA genes were identified. Some of miRNAs were found to be Hessian fly-specific and their expression was affected by host plant genotypes. The results provide a foundation for future research that may eventually lead to new ways for Hessian fly management.

Technical Abstract: MicroRNAs (miRNAs) are small noncoding RNAs that play critical roles in regulating gene expression post transcription. Gall midges are a large group of insects that are of economical importance and also possess fascinating biological traits. In this study, we systematically analyzed miRNAs from the gall midge Mayetiola destructor, commonly known as 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. The dramatic expansion of similar miRNAs provides a unique system to study functional relation among miRNA iso-genes and sequence specificity between small changes in miRNAs and changes in target mRNAs. Microarray analyses revealed the expression of miRNA genes were strictly regulated during Hessian fly larval development and many miRNA genes were affected by host genotypes. These results provide a foundation for further studies to elucidate miRNA functions in gall midges and for identification of miRNA genes for potential pest control through transgenic approach.