Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes

Bibliographic Details
Main Author: Abrahim, Mayla
Publication Date: 2022
Other Authors: Machado, Edson, Alvarez-Valín, Fernando, Miranda, Antonio Basílio de, Catanho, Marcos
Format: Article
Language: eng
Source: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.1093/gbe/evac142
Download full: https://arca.fiocruz.br/handle/icict/56027
Summary: Fundação Oswaldo Cruz. Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos. Instituto de Tecnologia em Imunobiológicos. Laboratório de Tecnologia Imunológica. Rio de Janeiro, RJ, Brasil.
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spelling Abrahim, MaylaMachado, EdsonAlvarez-Valín, FernandoMiranda, Antonio Basílio deCatanho, Marcos2022-12-17T19:33:28Z2022-12-17T19:33:28Z2022ABRAHIM, Mayla et al. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes. Genome Biol. Evol., v. 14, n. 10. p. 1 - 14, Oct. 2022.2482-500Xhttps://arca.fiocruz.br/handle/icict/5602710.1093/gbe/evac142engOxford University PressGenômicaTripanosomatídeosPesquisa de homologiaAlinhamento de sequênciaGenomicsTrypanosomatidsHomology searchSequence alignmentUncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos. Instituto de Tecnologia em Imunobiológicos. Laboratório de Tecnologia Imunológica. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactérias. Rio de Janeiro, RJ, Brasil.Universidad de la República del Uruguay. Unidad de Genómica Evolutiva, Sección Biomatemática. Montevideo, Uruguay.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genética Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil.Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://arca.fiocruz.br/bitstreams/1cda0da9-b777-44e2-b9b8-7f3132d43add/download5a560609d32a3863062d77ff32785d58MD51falseAnonymousREADORIGINALMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdfMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdfapplication/pdf642176https://arca.fiocruz.br/bitstreams/bc7e92e5-8726-4d03-8486-861d32806cad/downloadda4ec2f605ff2b7931d0b1980a90f130MD52trueAnonymousREADTEXTMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdf.txtMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdf.txtExtracted texttext/plain74196https://arca.fiocruz.br/bitstreams/371606bb-0e5d-4c18-aeab-cc1f657f7d24/download47ef8af7350a7183a194fb19ee2c8602MD57falseAnonymousREADTHUMBNAILMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdf.jpgMaylaAbrahim_MarcosCatanho_etal_IOC_2022.pdf.jpgGenerated Thumbnailimage/jpeg5035https://arca.fiocruz.br/bitstreams/528f8f83-1049-4702-8268-b7c6325cce33/download9f27dc43ac8ce09b6ff370bb2c689079MD58falseAnonymousREADicict/560272025-07-29 18:53:01.806open.accessoai:arca.fiocruz.br:icict/56027https://arca.fiocruz.brRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352025-07-29T21:53:01Repositório Institucional da FIOCRUZ (ARCA) - 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dc.title.none.fl_str_mv Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
title Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
spellingShingle Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
Abrahim, Mayla
Genômica
Tripanosomatídeos
Pesquisa de homologia
Alinhamento de sequência
Genomics
Trypanosomatids
Homology search
Sequence alignment
title_short Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
title_full Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
title_fullStr Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
title_full_unstemmed Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
title_sort Uncovering pseudogenes and intergenic protein-coding sequences in TriTryps’ genomes
author Abrahim, Mayla
author_facet Abrahim, Mayla
Machado, Edson
Alvarez-Valín, Fernando
Miranda, Antonio Basílio de
Catanho, Marcos
author_role author
author2 Machado, Edson
Alvarez-Valín, Fernando
Miranda, Antonio Basílio de
Catanho, Marcos
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Abrahim, Mayla
Machado, Edson
Alvarez-Valín, Fernando
Miranda, Antonio Basílio de
Catanho, Marcos
dc.subject.other.none.fl_str_mv Genômica
Tripanosomatídeos
Pesquisa de homologia
Alinhamento de sequência
topic Genômica
Tripanosomatídeos
Pesquisa de homologia
Alinhamento de sequência
Genomics
Trypanosomatids
Homology search
Sequence alignment
dc.subject.en.none.fl_str_mv Genomics
Trypanosomatids
Homology search
Sequence alignment
description Fundação Oswaldo Cruz. Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos. Instituto de Tecnologia em Imunobiológicos. Laboratório de Tecnologia Imunológica. Rio de Janeiro, RJ, Brasil.
publishDate 2022
dc.date.accessioned.fl_str_mv 2022-12-17T19:33:28Z
dc.date.available.fl_str_mv 2022-12-17T19:33:28Z
dc.date.issued.fl_str_mv 2022
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 ABRAHIM, Mayla et al. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes. Genome Biol. Evol., v. 14, n. 10. p. 1 - 14, Oct. 2022.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/56027
dc.identifier.issn.none.fl_str_mv 2482-500X
dc.identifier.doi.none.fl_str_mv 10.1093/gbe/evac142
identifier_str_mv ABRAHIM, Mayla et al. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes. Genome Biol. Evol., v. 14, n. 10. p. 1 - 14, Oct. 2022.
2482-500X
10.1093/gbe/evac142
url https://arca.fiocruz.br/handle/icict/56027
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)
collection Repositório Institucional da FIOCRUZ (ARCA)
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repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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