Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2018.00046 http://hdl.handle.net/11449/163887 |
Resumo: | The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F-ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme. |
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Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencingaquaculturegenetic structureNGSPirapitingaSerrasalmidaeThe pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F-ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)PROPE/UNESPSao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, BrazilUniv Santiago Compostela, Vet Fac, Lugo, SpainSao Paulo State Univ, Sch Sci, Bauru, BrazilSao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, BrazilSao Paulo State Univ, Sch Sci, Bauru, BrazilFAPESP: 2014/03772-7FAPESP: 2014/05732-2CNPq: 446779/2014-8CNPq: 305916/2015-7Frontiers Media SaUniversidade Estadual Paulista (Unesp)Univ Santiago CompostelaJorge, Paulo H. [UNESP]Mastrochirico-Filho, Vito A. [UNESP]Hata, Milene E. [UNESP]Mendes, Natalia J. [UNESP]Ariede, Raquel B. [UNESP]Freitas, Milena Vieira de [UNESP]Vera, ManuelPorto-Foresti, Fabio [UNESP]Hashimoto, Diogo T. [UNESP]2018-11-26T17:48:18Z2018-11-26T17:48:18Z2018-02-22info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://dx.doi.org/10.3389/fgene.2018.00046Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 12 p., 2018.1664-8021http://hdl.handle.net/11449/16388710.3389/fgene.2018.00046WOS:000425778500001WOS000425778500001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers In Genetics2,274info:eu-repo/semantics/openAccess2024-04-09T15:10:54Zoai:repositorio.unesp.br:11449/163887Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-04-09T15:10:54Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
title |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
spellingShingle |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing Jorge, Paulo H. [UNESP] aquaculture genetic structure NGS Pirapitinga Serrasalmidae |
title_short |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
title_full |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
title_fullStr |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
title_full_unstemmed |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
title_sort |
Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing |
author |
Jorge, Paulo H. [UNESP] |
author_facet |
Jorge, Paulo H. [UNESP] Mastrochirico-Filho, Vito A. [UNESP] Hata, Milene E. [UNESP] Mendes, Natalia J. [UNESP] Ariede, Raquel B. [UNESP] Freitas, Milena Vieira de [UNESP] Vera, Manuel Porto-Foresti, Fabio [UNESP] Hashimoto, Diogo T. [UNESP] |
author_role |
author |
author2 |
Mastrochirico-Filho, Vito A. [UNESP] Hata, Milene E. [UNESP] Mendes, Natalia J. [UNESP] Ariede, Raquel B. [UNESP] Freitas, Milena Vieira de [UNESP] Vera, Manuel Porto-Foresti, Fabio [UNESP] Hashimoto, Diogo T. [UNESP] |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Univ Santiago Compostela |
dc.contributor.author.fl_str_mv |
Jorge, Paulo H. [UNESP] Mastrochirico-Filho, Vito A. [UNESP] Hata, Milene E. [UNESP] Mendes, Natalia J. [UNESP] Ariede, Raquel B. [UNESP] Freitas, Milena Vieira de [UNESP] Vera, Manuel Porto-Foresti, Fabio [UNESP] Hashimoto, Diogo T. [UNESP] |
dc.subject.por.fl_str_mv |
aquaculture genetic structure NGS Pirapitinga Serrasalmidae |
topic |
aquaculture genetic structure NGS Pirapitinga Serrasalmidae |
description |
The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F-ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:48:18Z 2018-11-26T17:48:18Z 2018-02-22 |
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/10.3389/fgene.2018.00046 Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 12 p., 2018. 1664-8021 http://hdl.handle.net/11449/163887 10.3389/fgene.2018.00046 WOS:000425778500001 WOS000425778500001.pdf |
url |
http://dx.doi.org/10.3389/fgene.2018.00046 http://hdl.handle.net/11449/163887 |
identifier_str_mv |
Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 12 p., 2018. 1664-8021 10.3389/fgene.2018.00046 WOS:000425778500001 WOS000425778500001.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers In Genetics 2,274 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
12 application/pdf |
dc.publisher.none.fl_str_mv |
Frontiers Media Sa |
publisher.none.fl_str_mv |
Frontiers Media Sa |
dc.source.none.fl_str_mv |
Web of Science 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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_version_ |
1799964682628366336 |