Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach

Detalhes bibliográficos
Autor(a) principal: Silva, Esdras Matheus Gomes da
Data de Publicação: 2022
Outros Autores: Rebello, Karina Mastropasqua, Choi, Young-Jun, Gregorio, Vitor, Paschoal, Alexandre Rossi, Mitreva, Makedonka, McKerrow, James H., Neves-Ferreira, Ana Gisele da Costa, Passetti, Fabio
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/56446
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.
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spelling Silva, Esdras Matheus Gomes daRebello, Karina MastropasquaChoi, Young-JunGregorio, VitorPaschoal, Alexandre RossiMitreva, MakedonkaMcKerrow, James H.Neves-Ferreira, Ana Gisele da CostaPassetti, Fabio2023-01-12T14:59:45Z2023-01-12T14:59:45Z2022SILVA, Esdras Matheus Gomes da et al. Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach. Pathogens, v. 11, n. 1273, p. 1–16, 2022.2076-0817https://www.arca.fiocruz.br/handle/icict/5644610.3390/pathogens11111273porMDPIRNA-SeqNematodesncRNAsMass SpectrometryNematodaMolecular Sequence AnnotationRNA, Long NoncodingEspectrometría de MasasNematodosAnotación de Secuencia MolecularARN Largo no CodificanteSpectrométrie de masseNematodaAnnotation de séquence moléculaireARN long non codantEspectrometria de MassasNematoidesAnotação GênicaRNA Longo não CodificanteAngiostrongylusIdentification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approachinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Estudos Integrados em Protozoologia. Rio de Janeiro, RJ, Brasil.Department of Medicine. Washington University School of Medicine. St. Louis, USA.Universidade Tecnológica Federal do Paraná. Departamento de Ciência da Computação. Cornélio Procópio, PR, Brasil.Universidade Tecnológica Federal do Paraná. Departamento de Ciência da Computação. Cornélio Procópio, PR, Brasil.Department of Medicine. Washington University School of Medicine. St. Louis, USA.Center for Discovery and Innovation in Parasitic Diseases. Skaggs School of Pharmacy and Pharmaceutical Sciences. University of California, San Diego, USA.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain.info: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/56446/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALpathogens-11-01273ok.pdfpathogens-11-01273ok.pdfapplication/pdf2721894https://www.arca.fiocruz.br/bitstream/icict/56446/2/pathogens-11-01273ok.pdfe60182a0fa05ec1ba78bc5635fd8140fMD52icict/564462023-01-12 11:59:47.236oai:www.arca.fiocruz.br:icict/56446Q0VTU8ODTyBOw4NPIEVYQ0xVU0lWQSBERSBESVJFSVRPUyBBVVRPUkFJUwoKQW8gYWNlaXRhciBvcyBURVJNT1MgZSBDT05EScOHw5VFUyBkZXN0YSBDRVNTw4NPLCBvIEFVVE9SIGUvb3UgVElUVUxBUiBkZSBkaXJlaXRvcwphdXRvcmFpcyBzb2JyZSBhIE9CUkEgZGUgcXVlIHRyYXRhIGVzdGUgZG9jdW1lbnRvOgoKKDEpIENFREUgZSBUUkFOU0ZFUkUsIHRvdGFsIGUgZ3JhdHVpdGFtZW50ZSwgw6AgRklPQ1JVWiAtIEZVTkRBw4fDg08gT1NXQUxETyBDUlVaLCBlbQpjYXLDoXRlciBwZXJtYW5lbnRlLCBpcnJldm9nw6F2ZWwgZSBOw4NPIEVYQ0xVU0lWTywgdG9kb3Mgb3MgZGlyZWl0b3MgcGF0cmltb25pYWlzIE7Dg08KQ09NRVJDSUFJUyBkZSB1dGlsaXphw6fDo28gZGEgT0JSQSBhcnTDrXN0aWNhIGUvb3UgY2llbnTDrWZpY2EgaW5kaWNhZGEgYWNpbWEsIGluY2x1c2l2ZSBvcyBkaXJlaXRvcwpkZSB2b3ogZSBpbWFnZW0gdmluY3VsYWRvcyDDoCBPQlJBLCBkdXJhbnRlIHRvZG8gbyBwcmF6byBkZSBkdXJhw6fDo28gZG9zIGRpcmVpdG9zIGF1dG9yYWlzLCBlbQpxdWFscXVlciBpZGlvbWEgZSBlbSB0b2RvcyBvcyBwYcOtc2VzOwoKKDIpIEFDRUlUQSBxdWUgYSBjZXNzw6NvIHRvdGFsIG7Do28gZXhjbHVzaXZhLCBwZXJtYW5lbnRlIGUgaXJyZXZvZ8OhdmVsIGRvcyBkaXJlaXRvcyBhdXRvcmFpcwpwYXRyaW1vbmlhaXMgbsOjbyBjb21lcmNpYWlzIGRlIHV0aWxpemHDp8OjbyBkZSBxdWUgdHJhdGEgZXN0ZSBkb2N1bWVudG8gaW5jbHVpLCBleGVtcGxpZmljYXRpdmFtZW50ZSwKb3MgZGlyZWl0b3MgZGUgZGlzcG9uaWJpbGl6YcOnw6NvIGUgY29tdW5pY2HDp8OjbyBww7pibGljYSBkYSBPQlJBLCBlbSBxdWFscXVlciBtZWlvIG91IHZlw61jdWxvLAppbmNsdXNpdmUgZW0gUmVwb3NpdMOzcmlvcyBEaWdpdGFpcywgYmVtIGNvbW8gb3MgZGlyZWl0b3MgZGUgcmVwcm9kdcOnw6NvLCBleGliacOnw6NvLCBleGVjdcOnw6NvLApkZWNsYW1hw6fDo28sIHJlY2l0YcOnw6NvLCBleHBvc2nDp8OjbywgYXJxdWl2YW1lbnRvLCBpbmNsdXPDo28gZW0gYmFuY28gZGUgZGFkb3MsIHByZXNlcnZhw6fDo28sIGRpZnVzw6NvLApkaXN0cmlidWnDp8OjbywgZGl2dWxnYcOnw6NvLCBlbXByw6lzdGltbywgdHJhZHXDp8OjbywgZHVibGFnZW0sIGxlZ2VuZGFnZW0sIGluY2x1c8OjbyBlbSBub3ZhcyBvYnJhcyBvdQpjb2xldMOibmVhcywgcmV1dGlsaXphw6fDo28sIGVkacOnw6NvLCBwcm9kdcOnw6NvIGRlIG1hdGVyaWFsIGRpZMOhdGljbyBlIGN1cnNvcyBvdSBxdWFscXVlciBmb3JtYSBkZQp1dGlsaXphw6fDo28gbsOjbyBjb21lcmNpYWw7CgooMykgUkVDT05IRUNFIHF1ZSBhIGNlc3PDo28gYXF1aSBlc3BlY2lmaWNhZGEgY29uY2VkZSDDoCBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPCkNSVVogbyBkaXJlaXRvIGRlIGF1dG9yaXphciBxdWFscXVlciBwZXNzb2Eg4oCTIGbDrXNpY2Egb3UganVyw61kaWNhLCBww7pibGljYSBvdSBwcml2YWRhLCBuYWNpb25hbCBvdQplc3RyYW5nZWlyYSDigJMgYSBhY2Vzc2FyIGUgdXRpbGl6YXIgYW1wbGFtZW50ZSBhIE9CUkEsIHNlbSBleGNsdXNpdmlkYWRlLCBwYXJhIHF1YWlzcXVlcgpmaW5hbGlkYWRlcyBuw6NvIGNvbWVyY2lhaXM7CgooNCkgREVDTEFSQSBxdWUgYSBvYnJhIMOpIGNyaWHDp8OjbyBvcmlnaW5hbCBlIHF1ZSDDqSBvIHRpdHVsYXIgZG9zIGRpcmVpdG9zIGFxdWkgY2VkaWRvcyBlIGF1dG9yaXphZG9zLApyZXNwb25zYWJpbGl6YW5kby1zZSBpbnRlZ3JhbG1lbnRlIHBlbG8gY29udGXDumRvIGUgb3V0cm9zIGVsZW1lbnRvcyBxdWUgZmF6ZW0gcGFydGUgZGEgT0JSQSwKaW5jbHVzaXZlIG9zIGRpcmVpdG9zIGRlIHZveiBlIGltYWdlbSB2aW5jdWxhZG9zIMOgIE9CUkEsIG9icmlnYW5kby1zZSBhIGluZGVuaXphciB0ZXJjZWlyb3MgcG9yCmRhbm9zLCBiZW0gY29tbyBpbmRlbml6YXIgZSByZXNzYXJjaXIgYSBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPIENSVVogZGUKZXZlbnR1YWlzIGRlc3Blc2FzIHF1ZSB2aWVyZW0gYSBzdXBvcnRhciwgZW0gcmF6w6NvIGRlIHF1YWxxdWVyIG9mZW5zYSBhIGRpcmVpdG9zIGF1dG9yYWlzIG91CmRpcmVpdG9zIGRlIHZveiBvdSBpbWFnZW0sIHByaW5jaXBhbG1lbnRlIG5vIHF1ZSBkaXogcmVzcGVpdG8gYSBwbMOhZ2lvIGUgdmlvbGHDp8O1ZXMgZGUgZGlyZWl0b3M7CgooNSkgQUZJUk1BIHF1ZSBjb25oZWNlIGEgUG9sw610aWNhIEluc3RpdHVjaW9uYWwgZGUgQWNlc3NvIEFiZXJ0byBkYSBGSU9DUlVaIC0gRlVOREHDh8ODTwpPU1dBTERPIENSVVogZSBhcyBkaXJldHJpemVzIHBhcmEgbyBmdW5jaW9uYW1lbnRvIGRvIHJlcG9zaXTDs3JpbyBpbnN0aXR1Y2lvbmFsIEFSQ0EuCgpBIFBvbMOtdGljYSBJbnN0aXR1Y2lvbmFsIGRlIEFjZXNzbyBBYmVydG8gZGEgRklPQ1JVWiAtIEZVTkRBw4fDg08gT1NXQUxETyBDUlVaIHJlc2VydmEKZXhjbHVzaXZhbWVudGUgYW8gQVVUT1Igb3MgZGlyZWl0b3MgbW9yYWlzIGUgb3MgdXNvcyBjb21lcmNpYWlzIHNvYnJlIGFzIG9icmFzIGRlIHN1YSBhdXRvcmlhCmUvb3UgdGl0dWxhcmlkYWRlLCBzZW5kbyBvcyB0ZXJjZWlyb3MgdXN1w6FyaW9zIHJlc3BvbnPDoXZlaXMgcGVsYSBhdHJpYnVpw6fDo28gZGUgYXV0b3JpYSBlIG1hbnV0ZW7Dp8OjbwpkYSBpbnRlZ3JpZGFkZSBkYSBPQlJBIGVtIHF1YWxxdWVyIHV0aWxpemHDp8Ojby4KCkEgUG9sw610aWNhIEluc3RpdHVjaW9uYWwgZGUgQWNlc3NvIEFiZXJ0byBkYSBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPIENSVVoKcmVzcGVpdGEgb3MgY29udHJhdG9zIGUgYWNvcmRvcyBwcmVleGlzdGVudGVzIGRvcyBBdXRvcmVzIGNvbSB0ZXJjZWlyb3MsIGNhYmVuZG8gYW9zIEF1dG9yZXMKaW5mb3JtYXIgw6AgSW5zdGl0dWnDp8OjbyBhcyBjb25kacOnw7VlcyBlIG91dHJhcyByZXN0cmnDp8O1ZXMgaW1wb3N0YXMgcG9yIGVzdGVzIGluc3RydW1lbnRvcy4KRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-01-12T14:59:47Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
title Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
spellingShingle Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
Silva, Esdras Matheus Gomes da
RNA-Seq
Nematodes
ncRNAs
Mass Spectrometry
Nematoda
Molecular Sequence Annotation
RNA, Long Noncoding
Espectrometría de Masas
Nematodos
Anotación de Secuencia Molecular
ARN Largo no Codificante
Spectrométrie de masse
Nematoda
Annotation de séquence moléculaire
ARN long non codant
Espectrometria de Massas
Nematoides
Anotação Gênica
RNA Longo não Codificante
Angiostrongylus
title_short Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
title_full Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
title_fullStr Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
title_full_unstemmed Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
title_sort Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach
author Silva, Esdras Matheus Gomes da
author_facet Silva, Esdras Matheus Gomes da
Rebello, Karina Mastropasqua
Choi, Young-Jun
Gregorio, Vitor
Paschoal, Alexandre Rossi
Mitreva, Makedonka
McKerrow, James H.
Neves-Ferreira, Ana Gisele da Costa
Passetti, Fabio
author_role author
author2 Rebello, Karina Mastropasqua
Choi, Young-Jun
Gregorio, Vitor
Paschoal, Alexandre Rossi
Mitreva, Makedonka
McKerrow, James H.
Neves-Ferreira, Ana Gisele da Costa
Passetti, Fabio
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Silva, Esdras Matheus Gomes da
Rebello, Karina Mastropasqua
Choi, Young-Jun
Gregorio, Vitor
Paschoal, Alexandre Rossi
Mitreva, Makedonka
McKerrow, James H.
Neves-Ferreira, Ana Gisele da Costa
Passetti, Fabio
dc.subject.other.en_US.fl_str_mv RNA-Seq
Nematodes
ncRNAs
topic RNA-Seq
Nematodes
ncRNAs
Mass Spectrometry
Nematoda
Molecular Sequence Annotation
RNA, Long Noncoding
Espectrometría de Masas
Nematodos
Anotación de Secuencia Molecular
ARN Largo no Codificante
Spectrométrie de masse
Nematoda
Annotation de séquence moléculaire
ARN long non codant
Espectrometria de Massas
Nematoides
Anotação Gênica
RNA Longo não Codificante
Angiostrongylus
dc.subject.en.en_US.fl_str_mv Mass Spectrometry
Nematoda
Molecular Sequence Annotation
RNA, Long Noncoding
dc.subject.es.en_US.fl_str_mv Espectrometría de Masas
Nematodos
Anotación de Secuencia Molecular
ARN Largo no Codificante
dc.subject.fr.en_US.fl_str_mv Spectrométrie de masse
Nematoda
Annotation de séquence moléculaire
ARN long non codant
dc.subject.decs.en_US.fl_str_mv Espectrometria de Massas
Nematoides
Anotação Gênica
RNA Longo não Codificante
Angiostrongylus
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.
publishDate 2022
dc.date.issued.fl_str_mv 2022
dc.date.accessioned.fl_str_mv 2023-01-12T14:59:45Z
dc.date.available.fl_str_mv 2023-01-12T14:59:45Z
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 SILVA, Esdras Matheus Gomes da et al. Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach. Pathogens, v. 11, n. 1273, p. 1–16, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/56446
dc.identifier.issn.en_US.fl_str_mv 2076-0817
dc.identifier.doi.none.fl_str_mv 10.3390/pathogens11111273
identifier_str_mv SILVA, Esdras Matheus Gomes da et al. Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach. Pathogens, v. 11, n. 1273, p. 1–16, 2022.
2076-0817
10.3390/pathogens11111273
url https://www.arca.fiocruz.br/handle/icict/56446
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
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/56446/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/56446/2/pathogens-11-01273ok.pdf
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bitstream.checksumAlgorithm.fl_str_mv MD5
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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