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Start Over Author "Natália J. Mendes" Journal frontiers in genetics
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1. Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing

Author

Paulo H. Jorge, Vito A. Mastrochirico-Filho, Milene E. Hata, Natália J. Mendes, Raquel B. Ariede, Milena Vieira de Freitas, Manuel Vera, Fábio Porto-Foresti, and Diogo T. Hashimoto

Subjects
aquaculture, genetic structure, NGS, Pirapitinga, Serrasalmidae, Genetics, QH426-470
Abstract

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 FST 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.

Published
2018
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2. Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing

Author

Natália J. Mendes, Diogo Teruo Hashimoto, Vito A. Mastrochirico-Filho, Fábio Porto-Foresti, Manuel Vera, Milene Elissa Hata, Raquel B. Ariede, Milena V. Freitas, Paulo Henrique Jorge, Universidade Estadual Paulista (Unesp), Univ Santiago Compostela, Universidade de Santiago de Compostela. Centro de Investigación en Medicina Molecular e Enfermidades Crónicas, and Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física

Subjects
0106 biological sciences, 0301 basic medicine, lcsh:QH426-470, Fish farming, Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic variation, Genetics, genetic structure, Genetic variability, Genetics (clinical), Original Research, Piaractus brachypomus, Genetic diversity, biology.organism_classification, lcsh:Genetics, 030104 developmental biology, aquaculture, Genetic marker, NGS, Genetic structure, Molecular Medicine, Microsatellite, Pirapitinga, Serrasalmidae
Abstract

Made available in DSpace on 2018-11-26T17:48:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-22 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) PROPE/UNESP 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. Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Univ Santiago Compostela, Vet Fac, Lugo, Spain Sao Paulo State Univ, Sch Sci, Bauru, Brazil Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Sao Paulo State Univ, Sch Sci, Bauru, Brazil FAPESP: 2014/03772-7 FAPESP: 2014/05732-2 CNPq: 446779/2014-8 CNPq: 305916/2015-7

Published
2018

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