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Open Access Technical Note

Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer

Nikhil Kumar1, Todd Creasy1, Yezhou Sun1, Melissa Flowers1, Luke J Tallon1 and Julie C Dunning Hotopp12*

Author Affiliations

1 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

2 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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BMC Research Notes 2012, 5:230  doi:10.1186/1756-0500-5-230

Published: 14 May 2012

Abstract

Background

Numerous methods exist for enriching bacterial or mammalian mRNA prior to transcriptome experiments. Yet there persists a need for methods to enrich for mRNA in non-mammalian animal systems. For example, insects contain many important and interesting obligate intracellular bacteria, including endosymbionts and vector-borne pathogens. Such obligate intracellular bacteria are difficult to study by traditional methods. Therefore, genomics has greatly increased our understanding of these bacteria. Efficient subtraction methods are needed for removing both bacteria and insect rRNA in these systems to enable transcriptome-based studies.

Findings

A method is described that efficiently removes >95% of insect rRNA from total RNA samples, as determined by microfluidics and transcriptome sequencing. This subtraction yielded a 6.2-fold increase in mRNA abundance. Such a host rRNA-depletion strategy, in combination with bacterial rRNA depletion, is necessary to analyze transcription of obligate intracellular bacteria. Here, transcripts were identified that arise from a lateral gene transfer of an entire Wolbachia bacterial genome into a Drosophila ananassae chromosome. In this case, an rRNA depletion strategy is preferred over polyA-based enrichment since transcripts arising from bacteria-to-animal lateral gene transfer may not be poly-adenylated.

Conclusions

This enrichment method yields a significant increase in mRNA abundance when poly-A selection is not suitable. It can be used in combination with bacterial rRNA subtraction to enable experiments to simultaneously measure bacteria and insect mRNA in vector and endosymbiont biology experiments.

Keywords:
Wolbachia; Drosophila ananassae; RNASeq; Transcriptomics; Lateral gene transfer; Horizontal gene transfer; Endosymbiont; Insect vector