1. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing
- Author
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Horacio Schneider, Iracilda Sampaio, João L.S.G. Vianez, Jedson Ferreira Cardoso, Márcio Roberto Teixeira Nunes, Clayton Pereira Silva de Lima, Luciana Watanabe, and Fátima Gomes
- Subjects
0106 biological sciences ,Fish species ,Ontologia Gen?tica ,Gene Expression ,Muscle Proteins ,Aquaculture ,Tambaqui ,Biochemistry ,01 natural sciences ,Transcriptome ,Caraciformes / gen?tica ,Medicine and Health Sciences ,Musculoskeletal System ,Colossoma macropomum ,0303 health sciences ,Multidisciplinary ,Gene Ontologies ,Muscles ,High-Throughput Nucleotide Sequencing ,Agriculture ,Genomics ,Peixes / gen?tica ,Medicine ,Fish Farming ,Metabolic Pathways ,Anatomy ,Characiformes ,Manejo de Esp?cimes ,Transcriptome Analysis ,Research Article ,Fish farming ,Science ,Muscle Tissue ,Fisheries ,Biology ,010603 evolutionary biology ,DNA sequencing ,03 medical and health sciences ,Genetics ,Animals ,030304 developmental biology ,Biology and Life Sciences ,Computational Biology ,Proteins ,Genome Analysis ,biology.organism_classification ,Fishery ,Aquicultura ,Biological Tissue ,Metabolism ,Skeletal Muscles - Abstract
Center of Technological Innovation (CIT), Evandro Chagas Institute (IEC) and National Council of Scientific and Technological Development (CNPq) (Bionorte Project: 550939/2010-5). Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Programa de P?s-Gradua??o em Virologia. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Institute of Coastal Studies. Laboratory of Genetics and Molecular Biology. Bragan?a, PA, Brazil. 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.
- Published
- 2019