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Open Access Highly Accessed Research article

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

Alan D Winter1*, William Weir1, Martin Hunt2, Matthew Berriman2, John S Gilleard3, Eileen Devaney1* and Collette Britton1*

Author Affiliations

1 Institute of Infection, Immunity and Inflammation; College of Medical, Veterinary and Life Sciences; University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK

2 Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

3 Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada

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BMC Genomics 2012, 13:4  doi:10.1186/1471-2164-13-4

Published: 4 January 2012

Abstract

Background

MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs are involved in regulating developmental programs of parasitic nematodes is currently unknown. Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question.

Results

The small RNAs from larval and adult stages of two parasitic species, Brugia pahangi and Haemonchus contortus, were identified using deep-sequencing and bioinformatic approaches. Comparative analysis to known miRNA sequences reveals that the majority of these miRNAs are novel. Some novel miRNAs are abundantly expressed and display developmental regulation, suggesting important functional roles. Despite the lack of conservation in the miRNA repertoire, genomic positioning of certain miRNAs within or close to specific coding genes is remarkably conserved across diverse species, indicating selection for these associations. Endogenous small-interfering RNAs and Piwi-interacting (pi)RNAs, which regulate gene and transposon expression, were also identified. piRNAs are expressed in adult stage H. contortus, supporting a conserved role in germline maintenance in some parasitic nematodes.

Conclusions

This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention.