Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing
Autor(a) principal: | |
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Data de Publicação: | 2017 |
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/3841 |
Resumo: | Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the “biological processes” domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools. |
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Gomes, FátimaWatanabe, LucianaNozawa, SérgioOliveira, LayannaCardoso, Jedson FerreiraVianez Júnior, João Lídio da Silva GonçalvesNunes, Márcio Roberto TeixeiraSchneider, HoracioSampaio, Iracilda2019-08-16T11:37:42Z2019-08-16T11:37:42Z2017GOMES, Fátima et al. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics, v. 109, n. 2, p. 67-74, Mar. 2017.1089-8646http://patua.iec.gov.br//handle/iec/384110.1016/j.ygeno.2017.02.001Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the “biological processes” domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.National Council for Scientific and Technological Development (CNPq) (Bionorte Projct: 550939/2010-5)Federal University of Pará - Campus of Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Federal University of Pará - Campus of Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Dow AgroSciences. Ribeirão Preto, SP, 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. Ananindeua, PA, Brasil.Federal University of Pará - Campus of Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.Federal University of Pará - Campus of Bragança. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragança, PA, Brazil.engElsevierIdentification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencinginfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePeixes / anatomia & histologiaCaraciformes / genéticaCaraciformes / metabolismoMicroRNAs / genéticaFígado / metabolismoPele / metabolismoTranscriptomaExpressão GênicaAnálise de Sequência de RNASequenciamento de Nucleotídeos em Larga EscalaBiologia ComputacionalEcossistema Amazônico (BR)info:eu-repo/semantics/openAccessreponame:Repositório Digital do Instituto Evandro Chagas (Patuá)instname:Instituto Evandro Chagas (IEC)instacron:IECORIGINALIdentification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing.pdfIdentification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing.pdfapplication/pdf1243149https://patua.iec.gov.br/bitstreams/01261421-61aa-4bc5-ac3d-595fff286413/download3da973cf0ae56d685c6e615285bbedc2MD51LICENSElicense.txtlicense.txttext/plain; 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dc.title.pt_BR.fl_str_mv |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
title |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
spellingShingle |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing Gomes, Fátima Peixes / anatomia & histologia Caraciformes / genética Caraciformes / metabolismo MicroRNAs / genética Fígado / metabolismo Pele / metabolismo Transcriptoma Expressão Gênica Análise de Sequência de RNA Sequenciamento de Nucleotídeos em Larga Escala Biologia Computacional Ecossistema Amazônico (BR) |
title_short |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
title_full |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
title_fullStr |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
title_full_unstemmed |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
title_sort |
Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing |
author |
Gomes, Fátima |
author_facet |
Gomes, Fátima Watanabe, Luciana Nozawa, Sérgio Oliveira, Layanna Cardoso, Jedson Ferreira Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Schneider, Horacio Sampaio, Iracilda |
author_role |
author |
author2 |
Watanabe, Luciana Nozawa, Sérgio Oliveira, Layanna Cardoso, Jedson Ferreira Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Schneider, Horacio Sampaio, Iracilda |
author2_role |
author author author author author author author author |
dc.contributor.author.fl_str_mv |
Gomes, Fátima Watanabe, Luciana Nozawa, Sérgio Oliveira, Layanna Cardoso, Jedson Ferreira Vianez Júnior, João Lídio da Silva Gonçalves Nunes, Márcio Roberto Teixeira Schneider, Horacio Sampaio, Iracilda |
dc.subject.decsPrimary.pt_BR.fl_str_mv |
Peixes / anatomia & histologia Caraciformes / genética Caraciformes / metabolismo MicroRNAs / genética Fígado / metabolismo Pele / metabolismo Transcriptoma Expressão Gênica Análise de Sequência de RNA Sequenciamento de Nucleotídeos em Larga Escala Biologia Computacional Ecossistema Amazônico (BR) |
topic |
Peixes / anatomia & histologia Caraciformes / genética Caraciformes / metabolismo MicroRNAs / genética Fígado / metabolismo Pele / metabolismo Transcriptoma Expressão Gênica Análise de Sequência de RNA Sequenciamento de Nucleotídeos em Larga Escala Biologia Computacional Ecossistema Amazônico (BR) |
description |
Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the “biological processes” domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools. |
publishDate |
2017 |
dc.date.issued.fl_str_mv |
2017 |
dc.date.accessioned.fl_str_mv |
2019-08-16T11:37:42Z |
dc.date.available.fl_str_mv |
2019-08-16T11:37:42Z |
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. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics, v. 109, n. 2, p. 67-74, Mar. 2017. |
dc.identifier.uri.fl_str_mv |
http://patua.iec.gov.br//handle/iec/3841 |
dc.identifier.issn.-.fl_str_mv |
1089-8646 |
dc.identifier.doi.-.fl_str_mv |
10.1016/j.ygeno.2017.02.001 |
identifier_str_mv |
GOMES, Fátima et al. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics, v. 109, n. 2, p. 67-74, Mar. 2017. 1089-8646 10.1016/j.ygeno.2017.02.001 |
url |
http://patua.iec.gov.br//handle/iec/3841 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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Elsevier |
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Elsevier |
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