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

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dc.contributor.authorAnderson, Leticiaen
dc.contributor.authorAmaral, Murilo S.en
dc.contributor.authorBeckedorff, Felipeen
dc.contributor.authorSilva, Lucas F.en
dc.contributor.authorDazzani, Biancaen
dc.contributor.authorOliveira, Katia C.en
dc.contributor.authorAlmeida, Giulliana T.en
dc.contributor.authorGomes, Monete R.en
dc.contributor.authorPires, David S.en
dc.contributor.authorSetubal, Joao C.en
dc.contributor.authorDeMarco, Ricardoen
dc.contributor.authorVerjovski-Almeida, Sergioen
dc.date.accessioned2019-08-12T17:01:44Zen
dc.date.available2019-08-12T17:01:44Zen
dc.date.issued2015-12en
dc.description.abstractBackground 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. Methodology/Principal findings 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/Significance 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.en
dc.description.notesThis work was supported by a grant from Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP grant number 2010/51687-8) to SVA and in part by a grant from the European Union's Seventh Framework Programme under grant agreement no. 602080. LA, MSA, FB, KCPO, GTA were supported by fellowships from FAPESP. SVA, JCS and RDM received established investigator fellowship awards from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brasil. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.description.sponsorshipFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2010/51687-8]; European Union's Seventh Framework Programme [602080]; FAPESP; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brasilen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pntd.0004334en
dc.identifier.issn1935-2735en
dc.identifier.issue12en
dc.identifier.othere0004334en
dc.identifier.pmid26719891en
dc.identifier.urihttp://hdl.handle.net/10919/93029en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherPLOSen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjecttranscriptome analysisen
dc.subjectmitochondrial importen
dc.subjectdifferential geneen
dc.subjectquality-controlen
dc.subjectnoncoding rnasen
dc.subjectproteinen
dc.subjectgenomeen
dc.subjectmicroarrayen
dc.subjectdatabaseen
dc.subjectfeaturesen
dc.titleSchistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seqen
dc.title.serialPLOS Neglected Tropical Diseasesen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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