In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development

Original Paper
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Abstract

Schistosomiasis is a neglected tropical disease caused by trematode of the genus Schistosoma. Successful reproductive development is critical for the production of eggs, which are responsible for host pathology and disease dissemination. Endogenous small non-coding RNAs play important roles in many biological processes such as protection against foreign pathogens, cell differentiation, and chromosomal stability by regulating target gene expression at the transcriptional and post-transcriptional levels. In this study, we performed in silico analysis of endogenous small non-coding RNAs in different stages, and sex of S. japonicum focusing on endogenous small interfering RNAs (endo-siRNAs) generated from transposable elements (TEs) and natural antisense transcripts (NATs). Both total and unique siRNA populations show 18–30 nt in length, but the predominant size was 20 nt and the leading first base was adenosine. Sense TE-derived endo-siRNAs reads were higher than antisense reads at different relative positions of TEs, whereas no such difference was observed for NAT-derived endo-siRNAs. TE- and NAT-derived endo-siRNAs were more enriched in the male compared to female worms, with the higher relative expression in early phase of pairing. Putative targets of endo-siRNAs indicated more of them in males (106 and 66) than in females (6 and 23) for TE- and NAT-derived endo-siRNAs, respectively. Our preliminary study revealed vital role of endo-siRNAs during the reproductive development of S. japonicum and provide clues for putative novel targets to suppress worm reproduction and direction for effective anti-schistosomal drug development.

Keywords

Schistosoma japonicum Small noncoding RNA Endo-siRNA Transposable element Natural antisense transcript 

Notes

Acknowledgements

This study was supported by National Natural Science Foundation of China (31472187 and 31672550), National Key Research and Development Program of China (2017YFD0501300), and The Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

436_2018_5830_MOESM1_ESM.pptx (77 kb)
Fig. S1. Pipeline for identification of novel endo-siRNA in S. japonicum. (PPTX 77 kb)
436_2018_5830_MOESM2_ESM.pptx (480 kb)
Fig. S2. Characteristic length and first base distribution of unique endo-siRNA from different libraries. Female: mixed female worm pool; Male: mixed male worm pool. (PPTX 479 kb)
436_2018_5830_MOESM3_ESM.pptx (31 kb)
Table S1 (PPTX 31 kb)
436_2018_5830_MOESM4_ESM.pptx (31 kb)
Table S2 (PPTX 31 kb)
436_2018_5830_MOESM5_ESM.xlsx (11 kb)
Data S1 This data file contains mRNA sources of NAT-derived endo-siRNAs. (XLSX 11 kb)
436_2018_5830_MOESM6_ESM.xlsx (34 kb)
Data S2 This data file contains the top 50 TE-derived male- and female-enriched endo-siRNAs. (XLSX 34 kb)
436_2018_5830_MOESM7_ESM.xlsx (30 kb)
Data S3 This data file contains the top 50 NAT-derived male and female-enriched endo-siRNAs. (XLSX 30 kb)
436_2018_5830_MOESM8_ESM.xlsx (30 kb)
Data S4 This data file contains target mRNAs for the 50 TE- and NAT-derived sex-enriched endo-siRNAs. (XLSX 29 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Shanghai Veterinary Research Institute, Chinese Academy of Agricultural SciencesKey Laboratory of Animal Parasitology, Ministry of AgricultureShanghaiChina
  2. 2.School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina

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