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

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.

MicroRNAs in parasitic diseases: Potential for diagnosis and targeting

“…A recent review includes the information on the specific sequences found in parasites and their homologies with miRNA sequences of other organisms [2]. After this review, the number of identified miRNA sequences in parasites in which miRNAs were already known has increased due to large scale sequencing experiments, and new miRNA sequences have been also described in parasites in which miRNAs had not been evidenced before (see http://www.mirbase.org/search.shtml; [12][13][14][15]; Fig. 1).…”

“…In the last five years, parasite nematodes have also been candidates of miRNA studies, e.g. Trichinella spiralis and Haemonchus contortus [24,25,15]. These studies have shown interesting relationships between changes in the miRNA microenvironment linked to specific parasite life-cycle stages, and between the promotion of drug resistance and the presence of defined miRNAs, among others.…”

Functional analysis of microRNA activity in Brugia malayi

“…Recent deep sequencing projects have revealed the presence of many miRNA homologues in nematode parasites (reviewed in (Britton et al, 2014)). These include Ascaris suum (Wang et al, 2011), Brugia pahangi (Winter et al, 2012), Dirofilaria immitis (Fu et al, 2013) and the human filarial parasite Brugia malayi (Poole et al, 2010, 2014). While some putative miRNAs in parasitic nematodes are highly conserved, a large proportion appear to be novel (Winter et al, 2012).…”

“…These include Ascaris suum (Wang et al, 2011), Brugia pahangi (Winter et al, 2012), Dirofilaria immitis (Fu et al, 2013) and the human filarial parasite Brugia malayi (Poole et al, 2010, 2014). While some putative miRNAs in parasitic nematodes are highly conserved, a large proportion appear to be novel (Winter et al, 2012). Furthermore, many of the putative parasitic nematode miRNAs are restricted to certain lifecycle stages, suggesting that they function in developmental control of gene expression (Winter et al, 2012).…”

“…While some putative miRNAs in parasitic nematodes are highly conserved, a large proportion appear to be novel (Winter et al, 2012). Furthermore, many of the putative parasitic nematode miRNAs are restricted to certain lifecycle stages, suggesting that they function in developmental control of gene expression (Winter et al, 2012). Other studies have suggested that the parasite miRNAs may play a role in adaptation to life in the vertebrate host (Britton et al, 2014) and possibly in the development of drug resistance (Devaney et al, 2010).…”