Meta-analysis of RNA-seq studies reveals genes responsible for life stage-dominant functions in Schistosoma mansoni

Background: Since the genome of the parasitic flatworm Schistosoma mansoni was sequenced in 2009, various RNA-seq studies have been conducted to investigate differential gene expression between certain life stages. Based on these studies, the overview of gene expression in all life stages can improve our understanding of S. mansoni genome biology. Methods: publicly available RNA-seq data covering all life stages and gonads were mapped to the latest S. mansoni genome. Read counts were normalised across all samples and differential expression analysis was preformed using the generalized linear model (GLM) approach. Results: we revealed for the first time the dissimilarities among all life stages. Genes that are abundantly-expressed in all life stages, as well as those preferentially-expressed in certain stage(s), were determined. The latter reveals genes responsible for stage-dominant functions of the parasite, which can be a guidance for the investigation and annotation of gene functions. In addition, distinct differential expression patterns were observed between adjacent life stages, which not only correlate well with original individual studies, but also provide additional information on changes in gene expression during parasite transitions. Furthermore, thirteen novel housekeeping genes across all life stages were identified, which is valuable for quantitative studies (e.g., qPCR). Conclusions: the meta-analysis provides valuable information on the expression and potential functions of S. mansoni genes across all life stages, and can facilitate basic as well as applied research for the community.