1. De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish
- Author
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Clayton Pereira Silva de Lima, Fátima Gomes, Iracilda Sampaio, Jedson Ferreira Cardoso, Luciana Watanabe, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, and Horacio Schneider
- Subjects
0106 biological sciences ,0301 basic medicine ,Male ,Serum Proteins ,Skin Neoplasms ,ved/biology.organism_classification_rank.species ,De novo transcriptome assembly ,Cell Membranes ,lcsh:Medicine ,Gene Expression ,01 natural sciences ,Biochemistry ,Transcriptome ,Medicine and Health Sciences ,lcsh:Science ,Skin Tumors ,Sex Characteristics ,Multidisciplinary ,Bacia Amaz?nica (BR) ,Pigmentation ,Liver Diseases ,Gene Ontologies ,Fishes ,High-Throughput Nucleotide Sequencing ,Genomics ,Oncology ,Liver ,Female ,Anatomy ,Cellular Structures and Organelles ,Transcriptome Analysis ,Research Article ,Transcriptoma / gen?tica ,Caracteres Sexuais ,Dermatology ,Gastroenterology and Hepatology ,Biology ,010603 evolutionary biology ,Sequenciamento Completo do Genoma / m?todos ,DNA sequencing ,03 medical and health sciences ,Pirarucu ,Arapaima ,Peixes / anatomia & histologia ,Genetics ,Animals ,Blast2GO ,ved/biology ,Gene Expression Profiling ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,Cancers and Neoplasms ,Proteins ,Membrane Proteins ,Molecular Sequence Annotation ,Cell Biology ,biology.organism_classification ,Genome Analysis ,Sexual dimorphism ,Fatty Liver ,030104 developmental biology ,Evolutionary biology ,Pyrosequencing ,lcsh:Q ,Arapaima gigas - Abstract
The study was funded by the 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. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. 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. Ananindeua, PA, Brasil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. Universidade Federal do Par? - Campus de Bragan?a. Instituto de Estudos Costeiros. Laborat?rio de Gen?tica e Biologia Molecular. Bragan?a, PA, Brazil. BACKGROUND: The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. RESULTS: Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. CONCLUSION: Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts
- Published
- 2018