Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Digital do Instituto Evandro Chagas (Patuá) |
Texto Completo: | http://patua.iec.gov.br//handle/iec/3834 |
Resumo: | BACKGROUND: The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. RESULTS: The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. CONCLUSION: In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management. |
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Gomes, FátimaWatanabe, LucianaVianez Júnior, João Lídio da Silva GonçalvesNunes, Márcio Roberto TeixeiraCardoso, Jedson FerreiraLima, ClaytonSchneider, HoracioSampaio, Iracilda2019-08-14T14:26:18Z2019-08-14T14:26:18Z2019GOMES, Fátima et al. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS ONE, v. 14, n. 2, e0212755, p. 1-23, Feb. 2019.1932-6203http://patua.iec.gov.br//handle/iec/383410.1371/journal.pone.0212755BACKGROUND: The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. RESULTS: The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. CONCLUSION: In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.Center of Technological Innovation (CIT), Evandro Chagas Institute (IEC) and National Council of Scientific and Technological Development (CNPq) (Bionorte Project: 550939/2010-5).Universidade Federal do Pará - Campus de Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Universidade Federal do Pará - Campus de Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Programa de Pós-Graduação em Virologia. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Universidade Federal do Pará - Campus de Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Universidade Federal do Pará - Campus de Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.engPublic Library of ScienceComparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencinginfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePeixes / genéticaOntologia GenéticaCaraciformes / genéticaColossoma macropomumTambaquiManejo de EspécimesAquiculturainfo:eu-repo/semantics/openAccessreponame:Repositório Digital do Instituto Evandro Chagas (Patuá)instname:Instituto Evandro Chagas (IEC)instacron:IECORIGINALComparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing.pdfComparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing.pdfapplication/pdf2458831https://patua.iec.gov.br/bitstreams/2aeec533-923b-42cc-bbf1-2e79455197c1/downloadae3840ec954f6f5c2754c919e3746d4cMD51LICENSElicense.txtlicense.txttext/plain; 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dc.title.pt_BR.fl_str_mv |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
title |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
spellingShingle |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing Gomes, Fátima Peixes / genética Ontologia Genética Caraciformes / genética Colossoma macropomum Tambaqui Manejo de Espécimes Aquicultura |
title_short |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
title_full |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
title_fullStr |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
title_full_unstemmed |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
title_sort |
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing |
author |
Gomes, Fátima |
author_facet |
Gomes, Fátima Watanabe, Luciana Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Cardoso, Jedson Ferreira Lima, Clayton Schneider, Horacio Sampaio, Iracilda |
author_role |
author |
author2 |
Watanabe, Luciana Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Cardoso, Jedson Ferreira Lima, Clayton Schneider, Horacio Sampaio, Iracilda |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Gomes, Fátima Watanabe, Luciana Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Cardoso, Jedson Ferreira Lima, Clayton Schneider, Horacio Sampaio, Iracilda |
dc.subject.decsPrimary.pt_BR.fl_str_mv |
Peixes / genética Ontologia Genética Caraciformes / genética Colossoma macropomum Tambaqui Manejo de Espécimes Aquicultura |
topic |
Peixes / genética Ontologia Genética Caraciformes / genética Colossoma macropomum Tambaqui Manejo de Espécimes Aquicultura |
description |
BACKGROUND: The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. RESULTS: The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. CONCLUSION: In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-08-14T14:26:18Z |
dc.date.available.fl_str_mv |
2019-08-14T14:26:18Z |
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 |
GOMES, Fátima et al. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS ONE, v. 14, n. 2, e0212755, p. 1-23, Feb. 2019. |
dc.identifier.uri.fl_str_mv |
http://patua.iec.gov.br//handle/iec/3834 |
dc.identifier.issn.-.fl_str_mv |
1932-6203 |
dc.identifier.doi.-.fl_str_mv |
10.1371/journal.pone.0212755 |
identifier_str_mv |
GOMES, Fátima et al. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS ONE, v. 14, n. 2, e0212755, p. 1-23, Feb. 2019. 1932-6203 10.1371/journal.pone.0212755 |
url |
http://patua.iec.gov.br//handle/iec/3834 |
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eng |
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eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
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openAccess |
dc.publisher.none.fl_str_mv |
Public Library of Science |
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Public Library of Science |
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IEC |
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Repositório Digital do Instituto Evandro Chagas (Patuá) |
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Repositório Digital do Instituto Evandro Chagas (Patuá) |
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