Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing

Autor: Horacio Schneider, Iracilda Sampaio, João L.S.G. Vianez, Jedson Ferreira Cardoso, Márcio Roberto Teixeira Nunes, Clayton Pereira Silva de Lima, Luciana Watanabe, Fátima Gomes
Jazyk: angličtina
Rok vydání: 2019
Předmět:
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
Zdroj: PLoS ONE, Vol 14, Iss 2, p e0212755 (2019)
Repositório Digital do Instituto Evandro Chagas (Patuá)
Instituto Evandro Chagas (IEC)
instacron:IEC
PLoS ONE
ISSN: 1932-6203
Popis: 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.
Databáze: OpenAIRE
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