Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel.
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.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences; University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK. Alan.Winter@glasgow.ac.uk
Alan D
AD
Winter
William
W
Weir
Martin
M
Hunt
Matthew
M
Berriman
John S
JS
Gilleard
Eileen
E
Devaney
Collette
C
Britton
D000818:Animals; D017179:Brugia pahangi / Q000235:genetics* / Q000254:growth & development; D017173:Caenorhabditis elegans / Q000235:genetics / Q000254:growth & development; D016000:Cluster Analysis; D019295:Computational Biology; D017238:Genes, Helminth; D014644:Genetic Variation; D049751:Genome, Helminth / Q000235:genetics*; D006189:Haemonchus / Q000235:genetics* / Q000254:growth & development; D007814:Larva / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
D035683:MicroRNAs; D034741:RNA, Small Interfering