title: Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq.
abstract: BACKGROUND
  Schistosomiasis 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.
  
  
  RESULTS
  To 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
  Large-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.
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Letícia
authors.initials: L
authors.lastname: Anderson
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.|Instituto Butantan, São Paulo, SP, Brazil.
authors.forename: Murilo S
authors.initials: MS
authors.lastname: Amaral
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Felipe
authors.initials: F
authors.lastname: Beckedorff
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Lucas F
authors.initials: LF
authors.lastname: Silva
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Bianca
authors.initials: B
authors.lastname: Dazzani
authors.affiliation: Núcleo de Enteroparasitas, Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, São Paulo, SP, Brazil.
authors.forename: Katia C
authors.initials: KC
authors.lastname: Oliveira
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Giulliana T
authors.initials: GT
authors.lastname: Almeida
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Monete R
authors.initials: MR
authors.lastname: Gomes
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.|Instituto Butantan, São Paulo, SP, Brazil.
authors.forename: David S
authors.initials: DS
authors.lastname: Pires
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.|Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.affiliation: Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil.
authors.forename: Ricardo
authors.initials: R
authors.lastname: DeMarco
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.|Instituto Butantan, São Paulo, SP, Brazil.
authors.forename: Sergio
authors.initials: S
authors.lastname: Verjovski-Almeida
mesh_terms: D000349:Africa; D000818:Animals; D001483:Base Sequence; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D008877:Middle East; D008969:Molecular Sequence Data; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics; D012550:Schistosoma mansoni / Q000235:genetics*; D012555:Schistosomiasis mansoni / Q000469:parasitology*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018510:RNA, Helminth