The small RNA complement of adult Schistosoma haematobium

Abstract

Background: Blood flukes of the genus Schistosoma cause schistosomiasis-a neglected tropical disease (NTD) that affects more than 200 million people worldwide. Studies of schistosome genomes have improved our understanding of the molecular biology of flatworms, but most of them have focused largely on protein-coding genes. Small non-coding RNAs (sncRNAs) have been explored in selected schistosome species and are suggested to play essential roles in the post-transcriptional regulation of genes, and in modulating flatworm-host interactions. However, genome-wide small RNA data are currently lacking for key schistosomes including Schistosoma haematobium-the causative agent of urogenital schistosomiasis of humans.

Methodology: MicroRNAs (miRNAs) and other sncRNAs of male and female adults of S. haematobium and small RNA transcription levels were explored by deep sequencing, genome mapping and detailed bioinformatic analyses.

Principal findings: In total, 89 transcribed miRNAs were identified in S. haematobium-a similar complement to those reported for the congeners S. mansoni and S. japonicum. Of these miRNAs, 34 were novel, with no homologs in other schistosomes. Most miRNAs (n = 64) exhibited sex-biased transcription, suggestive of roles in sexual differentiation, pairing of adult worms and reproductive processes. Of the sncRNAs that were not miRNAs, some related to the spliceosome (n = 21), biogenesis of other RNAs (n = 3) or ribozyme functions (n = 16), whereas most others (n = 3798) were novel ('orphans') with unknown functions.

Conclusions: This study provides the first genome-wide sncRNA resource for S. haematobium, extending earlier studies of schistosomes. The present work should facilitate the future curation and experimental validation of sncRNA functions in schistosomes to enhance our understanding of post-transcriptional gene regulation and of the roles that sncRNAs play in schistosome reproduction, development and parasite-host cross-talk.

Fig 1. Frequency of read lengths of total and distinct (i.e. after merging redundant reads), quality-filtered small RNA reads representing adult male and female Schistosoma haematobium.

The median read length for each library is indicated with an asterisk.

Fig 2. The microRNAs (miRNAs) transcribed in male and female adults of Schistosoma haematobium that are homologous to known miRNA seeds, including those of S. mansoni and S. japonicum.

The miRNAs are ordered from highest to lowest transcription in the male adult, based on normalised read counts. Asterisks denote the five most highly transcribed miRNAs in the male and female adults; circles indicate miRNAs with homologous seeds in other schistosome species.

Fig 3. Small RNA clusters within the genome of Schistosoma haematobium.

(A) Small RNA clusters were identified in intergenic, intronic and exonic regions of the genome. Numbers represent mapped, complete/partial small RNA clusters in these regions on the sense and antisense strands, respectively. (B) Proportion of annotated repeat elements within the genome. (C) Proportion of clusters identified within annotated repeat elements of the genome. Clusters enriched within specific repeat families (one-sided Fisher’s exact test, p < 0.05) are marked with an asterisk. LINE, long interspersed nuclear element; LTR, long terminal repeat; SINE, short interspersed nuclear element.