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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.

ABSTRACT: 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.

SUBMITTER: Watanabe L

PROVIDER: S-EPMC6205615 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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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.

Watanabe Luciana L Gomes Fátima F Vianez João J Nunes Márcio M Cardoso Jedson J Lima Clayton C Schneider Horacio H Sampaio Iracilda I

PloS one 20181029 10

<h4>Background</h4>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.<h4>Results</h4>Four lib ...[more]

PMID: 30372461

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Project description:In air-breathing fish a reduction of gill surface area reduces the danger of losing oxygen taken up in the air-breathing organ (ABO) to hypoxic water, but it also reduces the surface area available for ion exchange, so that ion regulation may at least in part be transferred to other organs, like the kidney or the gut. In the air-breathing Arapaima gigas, gill lamellae regress as development proceeds, and starting as a water-breathing embryo Arapaima turns into an obligate air-breathing fish with proceeding development, suggesting that ion regulation is shifted away from the gills as the fish grows. In Arapaima the kidney projects medially into the ABO and thus, probably a unique situation among fishes, is in close contact to the gas of the ABO. We therefore hypothesized that the kidney would be predestined to adopt an increased importance for ion homeostasis, because the elevated ATP turnover connected to ion transport can easily be met by aerobic metabolism based on the excellent oxygen supply directly from the ABO. We also hypothesized that in gill tissue the reduced ion regulatory activity should result in a reduced metabolic activity. High metabolic activity and exposure to high oxygen tensions are connected to the production of reactive oxygen species (ROS), therefore the tissues exposed to these conditions should have a high ROS defense capacity. Using in vitro studies, we assessed metabolic activity and ROS production of gill, kidney and ABO tissue, and determined the activity of ROS degrading enzymes in small (~ 5g, 2-3 weeks old) and larger (~ 670 g, 3-4 months old) A. gigas. Comparing the three tissues revealed that kidney tissue oxygen uptake by far exceeded the uptake measured in gill tissue or ABO. ROS production was particularly high in gill tissue, and all three tissues had a high capacity to degrade ROS. Gill tissue was characterized by high activities of enzymes involved in the glutathione pathway to degrade ROS. By contrast, the tissues of the ABO and in particular the kidney were characterized by high catalase activities, revealing different, tissue-specific strategies in ROS defense in this species. Overall the differences in the activity of cells taken from small and larger fish were not as pronounced as expected, while at the tissue level the metabolic activity of kidney cells by far exceeded the activity of ABO and gill cells.

Project description:With the intensification of fish farming, the amount of residues also increased. One of the by-products generated is leather. However, several factors influence its quality, among them, the types of tanning used. Paiche (Arapaima gigas) is the largest freshwater fish in the world, and therefore has great potential in the use of leather, in addition to being one of the most cultivated fish in the Rondônia state. The aimed was to evaluate the physicomechanical resistance, histological and morphological aspects in different directions of the fibers of the paiche to evaluate the tanning with chromium oxide and vegetable tannin. Paiches with an average weight of 12.0 kg were used, skins were made and tanned using chromium and vegetable tannin as techniques. After tanning, 20 specimens were removed in longitudinal, transverse and diagonal directions to the fish body, to determine resistance in dynamometer and leather for histological analysis, scanning electron microscopy and physical-chemical analysis. The average thickness of the specimens of the leathers ranged 1.79mm to 2.82mm, in addition, there was no interaction between the type of tanning agent and the directions obtained for strength, traction and elongation. Regarding the progressive tearing test, there was also no interaction effect. However, the defined factors had relevant differences for the maximum and average amount applied, and the leathers tanned with vegetable tannin expanded to larger dimensions 110.19 and 85.52 N. According to the images obtained by histology and scanning microscopy, they presented that in the longitudinal and transverse direction the collagen fibers are presented in layers parallel to the leather surface and in the diagonal direction the interlacing is more intense, that is, in addition to the overlapping layers intercalated thinner, close to the surface, fiber bundles can also be seen crossing each other. It is concluded that leathers tanned with vegetable tannin have less resistance than leathers tanned with chromium salts for traction to rupture and greater resistance to tear.

Dataset Information

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.

Publications

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.

Similar Datasets

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