Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi

Detalhes bibliográficos
Autor(a) principal: Dıaz-Viraque, Florencia
Data de Publicação: 2019
Outros Autores: Pita, Sebastian, Greif, Gonzalo, Souza, Rita de Cassia Moreira de, Iraola, Gregorio, Robello, Carlos
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/36210
Resumo: Laboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay.
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spelling Dıaz-Viraque, FlorenciaPita, SebastianGreif, GonzaloSouza, Rita de Cassia Moreira deIraola, GregorioRobello, Carlos2019-10-04T19:45:25Z2019-10-04T19:45:25Z2019DIAZ-VIRAQUE, Florencia et al. Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi. Genome Biology and Evolution, v. 11, n. 7, p. 1952-1957, 2019.1759-6653https://www.arca.fiocruz.br/handle/icict/3621010.1093/gbe/evz129engOxford University PressNanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruziinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleLaboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay.Laboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay / Seccion Genetica Evolutiva. Facultad de Ciencias. Universidad de la Republica. Montevideo, Uruguay.Laboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay.Fundação Oswaldo Cruz. Instituto Rene Rachou. Grupo de Pesquisa Triatomíneos. Belo Horizonte, MG, Brasil.Microbial Genomics Laboratory. Institut Pasteur Montevideo. Montevideo, Uruguay / Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile.Laboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay / Departamento de Bioquımica. Facultad de Medicina. Universidad de la Republica. Montevideo, Uruguay.Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation, and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ∼16 Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single-copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource because it now constitutes a high-quality assembly available for TcII (clade C), a prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of these parasites and reinforces the idea that T. cruzi is intraspecifically divided in three main clades. Finally, this work represents the introduction of Nanopore technology to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes.Trypanosoma cruziBereniceChagas diseaseOxford Nanopore TechnologiesHybrid assemblyProtozoan parasitesinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83082https://www.arca.fiocruz.br/bitstream/icict/36210/1/license.txt9193a7c197bc67acd023525e72a03240MD51ORIGINALNanopore Sequencing Significantly.pdfNanopore Sequencing Significantly.pdfapplication/pdf446955https://www.arca.fiocruz.br/bitstream/icict/36210/2/Nanopore%20Sequencing%20Significantly.pdf8f6eb5397f33dccb221216fe8bbc8e43MD52TEXTNanopore Sequencing Significantly.pdf.txtNanopore Sequencing Significantly.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
title Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
spellingShingle Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
Dıaz-Viraque, Florencia
Trypanosoma cruzi
Berenice
Chagas disease
Oxford Nanopore Technologies
Hybrid assembly
Protozoan parasites
title_short Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
title_full Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
title_fullStr Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
title_full_unstemmed Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
title_sort Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi
author Dıaz-Viraque, Florencia
author_facet Dıaz-Viraque, Florencia
Pita, Sebastian
Greif, Gonzalo
Souza, Rita de Cassia Moreira de
Iraola, Gregorio
Robello, Carlos
author_role author
author2 Pita, Sebastian
Greif, Gonzalo
Souza, Rita de Cassia Moreira de
Iraola, Gregorio
Robello, Carlos
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Dıaz-Viraque, Florencia
Pita, Sebastian
Greif, Gonzalo
Souza, Rita de Cassia Moreira de
Iraola, Gregorio
Robello, Carlos
dc.subject.en.pt_BR.fl_str_mv Trypanosoma cruzi
Berenice
Chagas disease
Oxford Nanopore Technologies
Hybrid assembly
Protozoan parasites
topic Trypanosoma cruzi
Berenice
Chagas disease
Oxford Nanopore Technologies
Hybrid assembly
Protozoan parasites
description Laboratory of Host Pathogen Interactions – UBM. Institut Pasteur de Montevideo. Montevideo, Uruguay.
publishDate 2019
dc.date.accessioned.fl_str_mv 2019-10-04T19:45:25Z
dc.date.available.fl_str_mv 2019-10-04T19:45:25Z
dc.date.issued.fl_str_mv 2019
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv DIAZ-VIRAQUE, Florencia et al. Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi. Genome Biology and Evolution, v. 11, n. 7, p. 1952-1957, 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/36210
dc.identifier.issn.pt_BR.fl_str_mv 1759-6653
dc.identifier.doi.none.fl_str_mv 10.1093/gbe/evz129
identifier_str_mv DIAZ-VIRAQUE, Florencia et al. Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi. Genome Biology and Evolution, v. 11, n. 7, p. 1952-1957, 2019.
1759-6653
10.1093/gbe/evz129
url https://www.arca.fiocruz.br/handle/icict/36210
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
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