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Gomes F, Watanabe L, Vianez J, Nunes M, Cardoso J, Lima C, Schneider H, Sampaio I. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS One 2019; 14:e0212755. [PMID: 30802266 PMCID: PMC6388931 DOI: 10.1371/journal.pone.0212755] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/10/2019] [Indexed: 12/13/2022] Open
Abstract
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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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
- * E-mail:
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
- Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Clayton Lima
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
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Nunes JDRDS, Liu S, Pértille F, Perazza CA, Villela PMS, de Almeida-Val VMF, Hilsdorf AWS, Liu Z, Coutinho LL. Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. Sci Rep 2017; 7:46112. [PMID: 28387238 PMCID: PMC5384230 DOI: 10.1038/srep46112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/06/2017] [Indexed: 11/11/2022] Open
Abstract
Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.
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Affiliation(s)
- José de Ribamar da Silva Nunes
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.,The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America.,Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, Brazil
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Fábio Pértille
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Caio Augusto Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, P.O. Box 411, 08701-970, Mogi das Cruzes, SP, Brazil
| | - Priscilla Marqui Schmidt Villela
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Vera Maria Fonseca de Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, Brazil.,University Nilton Lins, Aquaculture Graduate Program, Manaus, Amazonas, Brazil
| | | | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Luiz Lehmann Coutinho
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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