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Computational and transcriptional evidence for microRNAs in the honey bee genome

Daniel B Weaver1, Juan M Anzola2, Jay D Evans3, Jeffrey G Reid4, Justin T Reese2, Kevin L Childs28, Evgeny M Zdobnov59, Manoj P Samanta6, Jonathan Miller7 and Christine G Elsik2*

  • * Corresponding author: Christine G Elsik

  • † Equal contributors

Author Affiliations

1 Bee Power, LP, Lynn Grove Road, 16481 CR 319, Navasota, TX 77868 USA

2 Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA

3 Bee Research Laboratory, USDA-ARS, BARC-E, Beltsville, MD, USA

4 WM Keck Center for Interdisciplinary BioScience Training, Houston, TX 77005, USA

5 European Molecular Biology Laboratory, Meyerhofstr., Heidelberg, Germany

6 Systemix Institute, Los Altos, CA 94024, USA

7 Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA

8 The Institute for Genome Research, Rockville, MD 20850, USA

9 Department of Genetic Medicine and Development, University of Geneva Medical School (CMU), rue Michel-Servet 1, 1211 Geneva 4, Switzerland

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Genome Biology 2007, 8:R97  doi:10.1186/gb-2007-8-6-r97

Published: 1 June 2007



Non-coding microRNAs (miRNAs) are key regulators of gene expression in eukaryotes. Insect miRNAs help regulate the levels of proteins involved with development, metabolism, and other life history traits. The recently sequenced honey bee genome provides an opportunity to detect novel miRNAs in both this species and others, and to begin to infer the roles of miRNAs in honey bee development.


Three independent computational surveys of the assembled honey bee genome identified a total of 65 non-redundant candidate miRNAs, several of which appear to have previously unrecognized orthologs in the Drosophila genome. A subset of these candidate miRNAs were screened for expression by quantitative RT-PCR and/or genome tiling arrays and most predicted miRNAs were confirmed as being expressed in at least one honey bee tissue. Interestingly, the transcript abundance for several known and novel miRNAs displayed caste or age-related differences in honey bees. Genes in proximity to miRNAs in the bee genome are disproportionately associated with the Gene Ontology terms 'physiological process', 'nucleus' and 'response to stress'.


Computational approaches successfully identified miRNAs in the honey bee and indicated previously unrecognized miRNAs in the well-studied Drosophila melanogaster genome despite the 280 million year distance between these insects. Differentially transcribed miRNAs are likely to be involved in regulating honey bee development, and arguably in the extreme developmental switch between sterile worker bees and highly fertile queens.