Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/s12864-021-07513-5 http://hdl.handle.net/11449/206180 |
Resumo: | Background: Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression. Results: Regarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism. Conclusions: Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization. |
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Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing dataFishmiRNAomaSkeletal muscleBackground: Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression. Results: Regarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism. Conclusions: Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Department of Structural and Functional Biology Institute of Biosciences São Paulo State University – UNESPNinth of July University – UNINOVEDepartment of Cellular Computational and Integrative Biology – CIBIO University of TrentoUniversity of Western Sao Paulo – UNOESTEDepartment of Structural and Functional Biology Institute of Biosciences São Paulo State University – UNESPFAPESP: 2015/19985-2FAPESP: 2016/05009-4FAPESP: 2017/15708-0CNPq: 302656/2015-4Universidade Estadual Paulista (Unesp)Ninth of July University – UNINOVEUniversity of TrentoUniversity of Western Sao Paulo – UNOESTEFantinatti, Bruno E. A. [UNESP]Perez, Erika S. [UNESP]Zanella, Bruna T. T. [UNESP]Valente, Jéssica S. [UNESP]de Paula, Tassiana G. [UNESP]Mareco, Edson A.Carvalho, Robson F. [UNESP]Piazza, SilvanoDenti, Michela A.Dal-Pai-Silva, Maeli [UNESP]2021-06-25T10:27:54Z2021-06-25T10:27:54Z2021-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s12864-021-07513-5BMC Genomics, v. 22, n. 1, 2021.1471-2164http://hdl.handle.net/11449/20618010.1186/s12864-021-07513-52-s2.0-85103994898Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomicsinfo:eu-repo/semantics/openAccess2021-10-22T21:54:41Zoai:repositorio.unesp.br:11449/206180Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-22T21:54:41Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
title |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
spellingShingle |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data Fantinatti, Bruno E. A. [UNESP] Fish miRNAoma Skeletal muscle |
title_short |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
title_full |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
title_fullStr |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
title_full_unstemmed |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
title_sort |
Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data |
author |
Fantinatti, Bruno E. A. [UNESP] |
author_facet |
Fantinatti, Bruno E. A. [UNESP] Perez, Erika S. [UNESP] Zanella, Bruna T. T. [UNESP] Valente, Jéssica S. [UNESP] de Paula, Tassiana G. [UNESP] Mareco, Edson A. Carvalho, Robson F. [UNESP] Piazza, Silvano Denti, Michela A. Dal-Pai-Silva, Maeli [UNESP] |
author_role |
author |
author2 |
Perez, Erika S. [UNESP] Zanella, Bruna T. T. [UNESP] Valente, Jéssica S. [UNESP] de Paula, Tassiana G. [UNESP] Mareco, Edson A. Carvalho, Robson F. [UNESP] Piazza, Silvano Denti, Michela A. Dal-Pai-Silva, Maeli [UNESP] |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Ninth of July University – UNINOVE University of Trento University of Western Sao Paulo – UNOESTE |
dc.contributor.author.fl_str_mv |
Fantinatti, Bruno E. A. [UNESP] Perez, Erika S. [UNESP] Zanella, Bruna T. T. [UNESP] Valente, Jéssica S. [UNESP] de Paula, Tassiana G. [UNESP] Mareco, Edson A. Carvalho, Robson F. [UNESP] Piazza, Silvano Denti, Michela A. Dal-Pai-Silva, Maeli [UNESP] |
dc.subject.por.fl_str_mv |
Fish miRNAoma Skeletal muscle |
topic |
Fish miRNAoma Skeletal muscle |
description |
Background: Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression. Results: Regarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism. Conclusions: Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-06-25T10:27:54Z 2021-06-25T10:27:54Z 2021-12-01 |
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.uri.fl_str_mv |
http://dx.doi.org/10.1186/s12864-021-07513-5 BMC Genomics, v. 22, n. 1, 2021. 1471-2164 http://hdl.handle.net/11449/206180 10.1186/s12864-021-07513-5 2-s2.0-85103994898 |
url |
http://dx.doi.org/10.1186/s12864-021-07513-5 http://hdl.handle.net/11449/206180 |
identifier_str_mv |
BMC Genomics, v. 22, n. 1, 2021. 1471-2164 10.1186/s12864-021-07513-5 2-s2.0-85103994898 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1799965580554403840 |