Dataset Information

From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum.

ABSTRACT: The teleost fish tambaqui, Colossoma macropomum, is a valuable resource for the Brazillian aquaculture sector, representing more than one-quarter of the total production. In this context, the development of molecular tools is paramount to address and improve productivity, nutrition, and genetic breeding programs. In this study, we applied RNA-seq technology to produce the first comprehensive liver transcriptome in this species. Our analysis generated a gold standard transcriptome with a total of 43,098 transcripts, with an N50 of 1855 bp and the average length of 1312 bp. To functionally annotate the transcripts, the Trinotate pipeline together with several public databases were scrutinized. The blast-x analysis revealed more than 40,000 homologous match hits for each database (NCBI-Nr, Uniref90, Swissprot, Trembl), while the Kaas web server allowed the mapping of our transcripts to 380 kegg pathways. The dataset provided in this study entails a comprehensive molecular resource, which will be instrumental to further develop tambaqui aquaculture, specifically in the field of nutrigenomics.

SUBMITTER: Machado AM

PROVIDER: S-EPMC6660486 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum.

Machado André M AM Ferraz Renato R Ribeiro Ricardo do Amaral RDA Ozório Rodrigo R Castro L Filipe C LFC

Data in brief 20190307

The teleost fish tambaqui, Colossoma macropomum, is a valuable resource for the Brazillian aquaculture sector, representing more than one-quarter of the total production. In this context, the development of molecular tools is paramount to address and improve productivity, nutrition, and genetic breeding programs. In this study, we applied RNA-seq technology to produce the first comprehensive liver transcriptome in this species. Our analysis generated a gold standard transcriptome w ...[more]

PMID: 31372415

Similar Datasets

Project description:Climate change substantially affects biodiversity around the world, especially in the Amazon region, which is home to a significant portion of the world's biodiversity. Freshwater fishes are susceptible to increases in water temperature and variations in the concentrations of dissolved gases, especially oxygen and carbon dioxide. It is important to understand the mechanisms underlying the physiological and biochemical abilities of fishes to survive such environmental changes. In the present study, we applied RNA-Seq and de novo transcriptome sequencing to evaluate transcriptome alterations in tambaqui when exposed to five or fifteen days of the B1, A1B and A2 climate scenarios foreseen by the IPCC. The generated ESTs were assembled into 54,206 contigs. Gene ontology analysis and the STRING tool were then used to identify candidate protein domains, genes and gene families potentially responsible for the adaptation of tambaqui to climate changes. After sequencing eight RNA-Seq libraries, 32,512 genes were identified and mapped using the Danio rerio genome as a reference. In total, 236 and 209 genes were differentially expressed at five and fifteen days, respectively, including chaperones, energetic metabolism-related genes, translation initiation factors and ribosomal genes. Gene ontology enrichment analysis revealed that mitochondrion, protein binding, protein metabolic process, metabolic processes, gene expression, structural constituent of ribosome and translation were the most represented terms. In addition, 1,202 simple sequence repeats were detected, 88 of which qualified for primer design. These results show that cellular response to climate change in tambaqui is complex, involving many genes, and it may be controlled by different cues and transcription/translation regulation mechanisms. The data generated from this study provide a valuable resource for further studies on the molecular mechanisms involved in the adaptation of tambaqui and other closely related teleost species to climate change.

Project description:Purpose: The gene molecular network involved in teleost fish sex determination and differentiation is highly variable among species and even in some cases among populations of the same species. The objectives of the present study were to identify the period of gonadal sex differentiation in tambaqui juveniles, as well as the genes and pathways potentially involved in this process. Methods: Histological analysis of juveniles was carried out to establish a timeline of the gonadal differentiation in tambaqui. Based on that knowledge, ten juveniles were selected before the first evidence of histological sex differentiation and total RNA was extracted from their trunks and used for RNA-Sequencing and a subsequent de novo transcriptome assembly. Principal Component Analysis (PCA) of the whole transcriptome data was used to cluster samples into two distinct groups: putative males and putative females. Differential gene expression, functional annotation and gene enrichment were used to identify genes and pathways related to sex differentiation in tambaqui to which was applied the Mann-Whitney non-parametric t test (p <0.05) confirming the statistical significance of the expression dimorphism between the groups. Results: The first sign of histological sex differentiation in tambaqui was the formation of the ovarian cavity detected in individuals measuring about 40 mm in total length. Before the differentiation period, components of the Wnt / β-catenin pathway, fox and fst genes (p <0.05) suggest female sex development in the putative females, whereas antagonistic pathways (gsk3b, wt1 and fgfr2), sox9 and genes for androgen synthesis (p <0.05) are indicative of a male-like differentiation. Conclusions: Tambaqui juveniles prior to the morphological ovarian differentiation present the Wnt / β-catenin pathway exerting putative role on the sex differentiation target, either upregulated in female-like individuals, or antagonized in male-like individuals. Thus, the present work provides a molecular basis for future studies on the application of tambaqui monosex cultivation.

Dataset Information

From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum.

Publications

From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, <i>Colossoma macropomum</i>.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets