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

Alan D Winter,Martin Hunt,Collette Britton,Eileen Devaney,Matthew Berriman,John S Gilleard,William Weir

doi:10.1186/1471-2164-13-4

Abstract

BackgroundMicroRNAs (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.ResultsThe 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.ConclusionsThis 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.

Highlights

MicroRNAs 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
To enable identification of small RNAs we exploited the almost complete and annotated genome sequence data for B. malayi [31] and mapped B. pahangi sequences to this genome. Sequences identified in this manner were considered common to B. pahangi and B. malayi and, as such, are referred to as Brugia small RNAs
Short read sequence data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO) under series accession number GSE34539

Summary

Introduction

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. MicroRNAs (miRNAs) are small, non-coding RNAs that play key roles in regulating gene expression in animals, plants and viruses. The mature ~22-nucleotide single-stranded molecule is incorporated into an RNA-induced silencing complex (RISC), directing it to mRNA targets resulting miRNAs show temporally controlled and cell-specific patterns of expression [6,7,8], with the first level of regulation being transcriptional. Genetic analysis in the free-living nematode Caenorhabditis elegans led to the discovery of the first miRNA, lin-4, which controls hypodermal cell fate decisions during early larval development [17,18]. Function may only become apparent after detailed analysis, as demonstrated for C. elegans mir-1, which regulates synaptic signalling at neuromuscular junctions and influences sensitivity to levamisole [27]

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