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The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology

BACKGROUND: Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding of the relevant host-parasite interactions, and the possible treatments are l...

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Autores principales: Silva, Larissa Lopes, Marcet-Houben, Marina, Nahum, Laila Alves, Zerlotini, Adhemar, Gabaldón, Toni, Oliveira, Guilherme
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534613/
https://www.ncbi.nlm.nih.gov/pubmed/23148687
http://dx.doi.org/10.1186/1471-2164-13-617
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author Silva, Larissa Lopes
Marcet-Houben, Marina
Nahum, Laila Alves
Zerlotini, Adhemar
Gabaldón, Toni
Oliveira, Guilherme
author_facet Silva, Larissa Lopes
Marcet-Houben, Marina
Nahum, Laila Alves
Zerlotini, Adhemar
Gabaldón, Toni
Oliveira, Guilherme
author_sort Silva, Larissa Lopes
collection PubMed
description BACKGROUND: Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding of the relevant host-parasite interactions, and the possible treatments are limited by the emergence of resistant strains and the absence of a vaccine. The S. mansoni genome was completely sequenced and still under continuous annotation. Nevertheless, more than 45% of the encoded proteins remain without experimental characterization or even functional prediction. To improve our knowledge regarding the biology of this parasite, we conducted a proteome-wide evolutionary analysis to provide a broad view of the S. mansoni’s proteome evolution and to improve its functional annotation. RESULTS: Using a phylogenomic approach, we reconstructed the S. mansoni phylome, which comprises the evolutionary histories of all parasite proteins and their homologs across 12 other organisms. The analysis of a total of 7,964 phylogenies allowed a deeper understanding of genomic complexity and evolutionary adaptations to a parasitic lifestyle. In particular, the identification of lineage-specific gene duplications pointed to the diversification of several protein families that are relevant for host-parasite interaction, including proteases, tetraspanins, fucosyltransferases, venom allergen-like proteins, and tegumental-allergen-like proteins. In addition to the evolutionary knowledge, the phylome data enabled us to automatically re-annotate 3,451 proteins through a phylogenetic-based approach rather than solely sequence similarity searches. To allow further exploitation of this valuable data, all information has been made available at PhylomeDB (http://www.phylomedb.org). CONCLUSIONS: In this study, we used an evolutionary approach to assess S. mansoni parasite biology, improve genome/proteome functional annotation, and provide insights into host-parasite interactions. Taking advantage of a proteome-wide perspective rather than focusing on individual proteins, we identified that this parasite has experienced specific gene duplication events, particularly affecting genes that are potentially related to the parasitic lifestyle. These innovations may be related to the mechanisms that protect S. mansoni against host immune responses being important adaptations for the parasite survival in a potentially hostile environment. Continuing this work, a comparative analysis involving genomic, transcriptomic, and proteomic data from other helminth parasites, other parasites, and vectors will supply more information regarding parasite’s biology as well as host-parasite interactions.
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spelling pubmed-35346132013-01-03 The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology Silva, Larissa Lopes Marcet-Houben, Marina Nahum, Laila Alves Zerlotini, Adhemar Gabaldón, Toni Oliveira, Guilherme BMC Genomics Research Article BACKGROUND: Schistosoma mansoni is one of the causative agents of schistosomiasis, a neglected tropical disease that affects about 237 million people worldwide. Despite recent efforts, we still lack a general understanding of the relevant host-parasite interactions, and the possible treatments are limited by the emergence of resistant strains and the absence of a vaccine. The S. mansoni genome was completely sequenced and still under continuous annotation. Nevertheless, more than 45% of the encoded proteins remain without experimental characterization or even functional prediction. To improve our knowledge regarding the biology of this parasite, we conducted a proteome-wide evolutionary analysis to provide a broad view of the S. mansoni’s proteome evolution and to improve its functional annotation. RESULTS: Using a phylogenomic approach, we reconstructed the S. mansoni phylome, which comprises the evolutionary histories of all parasite proteins and their homologs across 12 other organisms. The analysis of a total of 7,964 phylogenies allowed a deeper understanding of genomic complexity and evolutionary adaptations to a parasitic lifestyle. In particular, the identification of lineage-specific gene duplications pointed to the diversification of several protein families that are relevant for host-parasite interaction, including proteases, tetraspanins, fucosyltransferases, venom allergen-like proteins, and tegumental-allergen-like proteins. In addition to the evolutionary knowledge, the phylome data enabled us to automatically re-annotate 3,451 proteins through a phylogenetic-based approach rather than solely sequence similarity searches. To allow further exploitation of this valuable data, all information has been made available at PhylomeDB (http://www.phylomedb.org). CONCLUSIONS: In this study, we used an evolutionary approach to assess S. mansoni parasite biology, improve genome/proteome functional annotation, and provide insights into host-parasite interactions. Taking advantage of a proteome-wide perspective rather than focusing on individual proteins, we identified that this parasite has experienced specific gene duplication events, particularly affecting genes that are potentially related to the parasitic lifestyle. These innovations may be related to the mechanisms that protect S. mansoni against host immune responses being important adaptations for the parasite survival in a potentially hostile environment. Continuing this work, a comparative analysis involving genomic, transcriptomic, and proteomic data from other helminth parasites, other parasites, and vectors will supply more information regarding parasite’s biology as well as host-parasite interactions. BioMed Central 2012-11-13 /pmc/articles/PMC3534613/ /pubmed/23148687 http://dx.doi.org/10.1186/1471-2164-13-617 Text en Copyright ©2012 Silva et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Silva, Larissa Lopes
Marcet-Houben, Marina
Nahum, Laila Alves
Zerlotini, Adhemar
Gabaldón, Toni
Oliveira, Guilherme
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title_full The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title_fullStr The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title_full_unstemmed The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title_short The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
title_sort schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534613/
https://www.ncbi.nlm.nih.gov/pubmed/23148687
http://dx.doi.org/10.1186/1471-2164-13-617
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