A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients

Detalhes bibliográficos
Autor(a) principal: Bourgard, Catarina
Data de Publicação: 2021
Outros Autores: Lopes, Stefanie C. P., Lacerda, Marcus V. G., Albrecht, Letusa, Costa, Fabio T. M.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/56919
Resumo: Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) e Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).
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spelling Bourgard, CatarinaLopes, Stefanie C. P.Lacerda, Marcus V. G.Albrecht, LetusaCosta, Fabio T. M.2023-02-07T14:18:41Z2023-02-07T14:18:41Z2021BOURGARD, Catarina et al. A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients. Scientific Reports, [s. l.], v. 11, n. 5089, p. 1-12, 2021.2045-2322https://www.arca.fiocruz.br/handle/icict/5691910.1038/s41598-021-84607-wFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) e Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).University of Campinas. Institute of Biology. Department of Genetics, Evolution, Microbiology and Immunology. Prof. Dr. Luiz Jacintho da Silva. Laboratory of Tropical Diseases. Campinas, SP, Brazil.Fundação Oswaldo Cruz. Instituto Leônidas & Maria Deane. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Instituto Leônidas & Maria Deane. Manaus, AM, Brasil.University of Campinas. Institute of Biology. Department of Genetics, Evolution, Microbiology and Immunology. Prof. Dr. Luiz Jacintho da Silva. Laboratory of Tropical Diseases. Campinas, SP, Brazil.University of Campinas. Institute of Biology. Department of Genetics, Evolution, Microbiology and Immunology. Prof. Dr. Luiz Jacintho da Silva. Laboratory of Tropical Diseases. Campinas, SP, Brazil.Plasmodium vivax is a world-threatening human malaria parasite, whose biology remains elusive. The unavailability of in vitro culture, and the difficulties in getting a high number of pure parasites makes RNA isolation in quantity and quality a challenge. Here, a methodological outline for RNA-seq from P. vivax isolates with low parasitemia is presented, combining parasite maturation and enrichment with efficient RNA extraction, yielding ~ 100 pg.µL−1 of RNA, suitable for SMART-Seq Ultra-Low Input RNA library and Illumina sequencing. Unbiased coding transcriptome of ~ 4 M reads was achieved for four patient isolates with ~ 51% of transcripts mapped to the P. vivax P01 reference genome, presenting heterogeneous profiles of expression among individual isolates. Amongst the most transcribed genes in all isolates, a parasite-staged mixed repertoire of conserved parasite metabolic, membrane and exported proteins was observed. Still, a quarter of transcribed genes remain functionally uncharacterized. In parallel, a P. falciparum Brazilian isolate was also analyzed and 57% of its transcripts mapped against IT genome. Comparison of transcriptomes of the two species revealed a common trophozoite-staged expression profile, with several homologous genes being expressed. Collectively, these results will positively impact vivax research improving knowledge of P. vivax biology.engA suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patientsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePlasmodium vivaxMalariainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/56919/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALBourgard _Catarina_etal_ILMD_2021.pdfBourgard _Catarina_etal_ILMD_2021.pdfapplication/pdf3071077https://www.arca.fiocruz.br/bitstream/icict/56919/2/Bourgard%20_Catarina_etal_ILMD_2021.pdf12796d1909443824b8053a8c689bed7bMD52icict/569192023-02-07 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dc.title.en_US.fl_str_mv A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
title A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
spellingShingle A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
Bourgard, Catarina
Plasmodium vivax
Malaria
title_short A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
title_full A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
title_fullStr A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
title_full_unstemmed A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
title_sort A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients
author Bourgard, Catarina
author_facet Bourgard, Catarina
Lopes, Stefanie C. P.
Lacerda, Marcus V. G.
Albrecht, Letusa
Costa, Fabio T. M.
author_role author
author2 Lopes, Stefanie C. P.
Lacerda, Marcus V. G.
Albrecht, Letusa
Costa, Fabio T. M.
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Bourgard, Catarina
Lopes, Stefanie C. P.
Lacerda, Marcus V. G.
Albrecht, Letusa
Costa, Fabio T. M.
dc.subject.en.en_US.fl_str_mv Plasmodium vivax
Malaria
topic Plasmodium vivax
Malaria
description Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) e Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2023-02-07T14:18:41Z
dc.date.available.fl_str_mv 2023-02-07T14:18:41Z
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 BOURGARD, Catarina et al. A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients. Scientific Reports, [s. l.], v. 11, n. 5089, p. 1-12, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/56919
dc.identifier.issn.en_US.fl_str_mv 2045-2322
dc.identifier.doi.none.fl_str_mv 10.1038/s41598-021-84607-w
identifier_str_mv BOURGARD, Catarina et al. A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax‑infected patients. Scientific Reports, [s. l.], v. 11, n. 5089, p. 1-12, 2021.
2045-2322
10.1038/s41598-021-84607-w
url https://www.arca.fiocruz.br/handle/icict/56919
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.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)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/56919/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/56919/2/Bourgard%20_Catarina_etal_ILMD_2021.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
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