Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq.
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 hep...
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ftdoajarticles:oai:doaj.org/article:4bcb57cc636243d38988a90afaa14338 2023-05-15T15:16:10+02:00 Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. 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 2015-12-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0004334 https://doaj.org/article/4bcb57cc636243d38988a90afaa14338 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4699917?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0004334 https://doaj.org/article/4bcb57cc636243d38988a90afaa14338 PLoS Neglected Tropical Diseases, Vol 9, Iss 12, p e0004334 (2015) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2015 ftdoajarticles https://doi.org/10.1371/journal.pntd.0004334 2022-12-31T12:17:08Z 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. 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/). ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 9 12 e0004334 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 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 Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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. 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/). ... |
format |
Article in Journal/Newspaper |
author |
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 |
author_facet |
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 |
author_sort |
Letícia Anderson |
title |
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
title_short |
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
title_full |
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
title_fullStr |
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
title_full_unstemmed |
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. |
title_sort |
schistosoma mansoni egg, adult male and female comparative gene expression analysis and identification of novel genes by rna-seq. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2015 |
url |
https://doi.org/10.1371/journal.pntd.0004334 https://doaj.org/article/4bcb57cc636243d38988a90afaa14338 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 9, Iss 12, p e0004334 (2015) |
op_relation |
http://europepmc.org/articles/PMC4699917?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0004334 https://doaj.org/article/4bcb57cc636243d38988a90afaa14338 |
op_doi |
https://doi.org/10.1371/journal.pntd.0004334 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
9 |
container_issue |
12 |
container_start_page |
e0004334 |
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1766346460096364544 |