Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq

Abstract

BackgroundSchistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas, Middle East and Africa. Adult female worms (mated to males) release eggs in the hepatic portal vasculature and are the principal cause of morbidity. Comparative separate transcriptomes of female and male adult worms were previously assessed with using microarrays and Serial Analysis of Gene Expression (SAGE), thus limiting the possibility of finding novel genes. Moreover, the egg transcriptome was analyzed only once with limited bacterially cloned cDNA libraries.Methodology/Principal findingsTo compare the gene expression of S. mansoni eggs, females, and males, we performed RNA-Seq on these three parasite forms using 454/Roche technology and reconstructed the transcriptome using Trinity de novo assembly. The resulting contigs were mapped to the genome and were cross-referenced with predicted Smp genes and H3K4me3 ChIP-Seq public data. For the first time, we obtained separate, unbiased gene expression profiles for S. mansoni eggs and female and male adult worms, identifying enriched biological processes and specific enriched functions for each of the three parasite forms. Transcripts with no match to predicted genes were analyzed for their protein-coding potential and the presence of an encoded conserved protein domain. A set of 232 novel protein-coding genes with putative functions related to reproduction, metabolism, and cell biogenesis was detected, which contributes to the understanding of parasite biology.Conclusions/SignificanceLarge-scale RNA-Seq analysis using de novo assembly associated with genome-wide information for histone marks in the vicinity of gene models constitutes a new approach to transcriptome analysis that has not yet been explored in schistosomes. Importantly, all data have been consolidated into a UCSC Genome Browser search- and download-tool (http://schistosoma.usp.br/). This database provides new ways to explore the schistosome genome and transcriptome and will facilitate molecular research on this important parasite.

A next-generation microarray further reveals stage-enriched gene expression pattern in the blood fluke Schistosoma japonicum

“…Thirdly, the screening criteria for stage-enriched genes may have varied among different studies. Nevertheless, we compared our data with these from previous Schistosoma transcriptome data [7, 13, 14, 23, 28] by manual checking. Globally, about 4.57, 10.07 and 12.97% genes enriched in cercariae, adult worms and eggs, respectively, were reported in previous studies (Additional files 4, 5 and 7: Tables S3, S4, S6).…”

“…In this respect, high-throughput technologies, such as microarrays [12–18], serial analysis of gene expression (SAGE) [19–21], digital gene expression (DGE) [22], and, more recently, RNAseq [23, 24] have been employed in the analysis of gene profiling in schistosomes. These pioneering investigations have provided unique information on developmental-enriched, gender-biased, tissue-specific, strain-specific and host-associated gene expression features within schistosomes [12, 14, 25–28], revealing critical insight on the biology of these parasites.…”

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

“…Due to its complex life cycle, this parasite is also an interesting model for investigations in the fields of genomics and transcriptomics [please refer to the following World Health Organization (WHO) website for a detailed view of schistosomes life cycle: http://www.who.int/schistosomiasis/epidemiology/en/]. High-throughput screenings using RNA-Seq have already shown that there are drastic changes in gene expression during parasite development, with thousands of differentially expressed genes identified in different life stages (4, 6–8). …”

“…One can navigate on those novel genes loci and check their architectures through the S. mansoni UCSC-like genome browser (http://schistosoma.usp.br/), which we developed previously (6, 7). Several hundreds of S. mansoni lincRNAs (SmLINC) showed traits for being functional (7), such as the presence of trimethylation on lysine 4 of histone H3 (H3K4me3) as an epigenetic mark at their transcription start sites (2878/7029), evolutionary conservation among Schistosoma haematobium and Schistosoma japonicum (3453/7029), and differential expression across five different life-cycle stages of the parasite (916/7029).…”

“…The Cytoscape software can be downloaded from http://www.cytoscape.org. The S. mansoni V5.2 annotated genome sequence (4) and the SmLINC genes loci (7) can be visualized in the S. mansoni UCSC-like genome browser (http://schistosoma.usp.br/), which we developed previously (6, 7). …”