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

Date Published: December 31, 2015

Publisher: Public Library of Science

Author(s): Letícia Anderson, Murilo S. Amaral, Felipe Beckedorff, Lucas F. Silva, Bianca Dazzani, Katia C. Oliveira, Giulliana T. Almeida, Monete R. Gomes, David S. Pires, João C. Setubal, Ricardo DeMarco, Sergio Verjovski-Almeida, Aaron R. Jex. http://doi.org/10.1371/journal.pntd.0004334

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.

Partial Text: Schistosomiasis is a parasitic disease caused by blood-dwelling worms of the genus Schistosoma. It is an important public health problem, with high morbidity and mortality in endemic countries. Over 230 million people worldwide are infected by Schistosoma spp., comprising three main species [1]; Schistosoma mansoni is the species responsible for infecting people in the Americas, Middle East and Africa [1]. The parasite has a complex life cycle that includes several morphological phenotypes in the intermediate Biomphalaria spp. snail host and in the human definitive host, with adult worms having separate sexes, and the mated female worms releasing hundreds of eggs daily in the mesenteric circulation of the human host [2].

The S. mansoni genome and transcriptome have been explored for the past decade [47], providing information related to the gene expression profiling and transcription regulation of certain life-cycle stages of the parasite. In this study we have obtained, for the first time, large-scale RNA-Seq separate profiles of S. mansoni females and males, as well as the egg-derived expression profile. We also used, for the first time, a combination of de novo transcriptome assembly with existing genome coordinates of predicted genes, along with newly mapped public ChIP-Seq data, which permitted the identification of novel putative S. mansoni genes. Because we have, for the first time, generated an individual gene profile for each of these three parasite forms, we explored this additional information by searching the literature for the possible functions of a selected set of genes most highly expressed in each form, as described below.

Source:

http://doi.org/10.1371/journal.pntd.0004334

 

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