Abstract
BackgroundmicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. The particular developmental and metabolic characteristics of cestode parasites highlight the importance of studying miRNA gene regulation in these organisms. Here, we perform a comprehensive analysis of miRNAs in the parasitic cestode Echinococcus canadensis G7, one of the causative agents of the neglected zoonotic disease cystic echinococcosis.MethodsSmall RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. For miRNA prediction, miRDeep2 core algorithm was used. The output list of candidate precursors was manually curated to generate a high confidence set of miRNAs. Differential expression analysis of miRNAs between stages or species was estimated with DESeq. Expression levels of selected miRNAs were validated using poly-A RT-qPCR.ResultsIn this study we used a high-throughput approach and found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed highly regulated miRNAs between life cycle stages, suggesting a role in maintaining the features of each developmental stage or in the regulation of developmental timing. In this work we characterize conserved and novel Echinococcus miRNAs which represent 30 unique miRNA families. Here we confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism.ConclusionsWe performed the first in-depth study profiling of small RNAs in the zoonotic parasite E. canadensis G7. We found that miRNAs are the preponderant small RNA silencing molecules, suggesting that these small RNAs could be an essential mechanism of gene regulation in this species. We also identified both parasite specific and divergent miRNAs which are potential biomarkers of infection. This study will provide valuable information for better understanding of the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-0686-8) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs, a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism
Small RNA library sequence analysis In order to explore the whole repertoire of miRNAs expressed by E. canadensis G7 and compare miRNA expression between stages, small RNA libraries from cyst walls (CWG7) and PS (PSG7) from E. canadensis G7 were sequenced using Illumina technology
The proportion of reads assigned to each category for CWG7, PS from E. canadensis G7 (PSG7) and PSG1 libraries can be observed in Figure 2A-C. miRNA reads were the most abundant category in PSG7 and PSG1 libraries accounting for 53% and 45% of total mapped reads, respectively
Summary
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. L. parasites display some unique characteristics such as the ability of the germinal layer to undergo practically unlimited asexual proliferation These parasites have a high degree of developmental plasticity which allows the PS to develop into an adult worm in the definitive host and to de-differentiate into secondary hydatid cysts if rupture and content leakage from the primary cyst occur within the intermediate host. E. canadensis G7 is highly adapted to pigs and wild boars and is able to infect humans [3,4] It differs from other members of the complex in morphology, development and genetic traits [5], including genomic organization and abundance of repetitive DNA elements [6], composition and sequence of antigen-coding genes such as Antigen B [7,8] and the vaccine antigen EG95 [9] which was recently shown to differ in antigenicity with EG95 from other species of E. granulosus s. This could help, in turn, to find new control strategies by discovering essential and specific molecules which could be considered as potential targets for therapy and/or diagnosis
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