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Integrative microRNAome analysis of muscle tissue of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu) and the hybrid, tambacu, based on next-generation sequencing data.

ABSTRACT: Integrative microRNAome analysis of muscle tissue of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu) and the hybrid, tambacu, based on next-generation sequencing data.

PROVIDER: PRJNA615184 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11423732.fastq.gz	Fastqsanger.gz
	SRR11423733.fastq.gz	Fastqsanger.gz
	SRR11423734.fastq.gz	Fastqsanger.gz
	SRR11423735.fastq.gz	Fastqsanger.gz
	SRR11423736.fastq.gz	Fastqsanger.gz

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Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on next-generation sequencing data.

Project description:BackgroundColossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms. Here, we used small RNA sequencing to examine global miRNA expression in the genotypes pacu (PC), tambaqui (TQ), and hybrid tambacu (TC), (Juveniles, n = 5 per genotype), to better understand the relationship between tambacu and its parental species, and also to clarify the mechanisms involved in tambacu muscle growth and maintenance based on miRNAs expression.ResultsRegarding differentially expressed (DE) miRNAs between the three genotypes, we observed 8 upregulated and 7 downregulated miRNAs considering TC vs. PC; 14 miRNAs were upregulated and 10 were downregulated considering TC vs. TQ, and 15 miRNAs upregulated and 9 were downregulated considering PC vs. TQ. The majority of the miRNAs showed specific regulation for each genotype pair, and no miRNA were shared between the 3 genotype pairs, in both up- and down-regulated miRNAs. Considering only the miRNAs with validated target genes, we observed the miRNAs miR-144-3p, miR-138-5p, miR-206-3p, and miR-499-5p. GO enrichment analysis showed that the main target genes for these miRNAs were grouped in pathways related to oxygen homeostasis, blood vessel modulation, and oxidative metabolism.ConclusionsOur global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization.

| S-EPMC8022549 | biostudies-literature

Piaractus mesopotamicus

Project description:Piaractus mesopotamicus overview

| PRJNA261983 | ENA

Amino acids and IGF1 regulation of fish muscle growth revealed by transcriptome and microRNAome integrative analyses of pacu (Piaractus mesopotamicus) myotubes [RNA-seq]

Project description:Amino acids (AA) and IGF1 have demonstrated to play essential roles in protein synthesis and fish muscle growth. The myoblast cell culture is useful to study the muscle regulation, and omics data have contributed enormously to understand its molecular biology. However, to our knowledge, no study has performed large-scale sequencing of fish cultured muscle cells stimulated with pro-growth signals. In this work, we obtained the transcriptome and microRNAome of pacu (Piaractus mesopotamicus) cultured myotubes treated with AA or IGF1. We identified 1228 and 534 genes differentially expressed by AA and IGF1. Enrichment analysis showed that AA treatment induced chromosomal changes, mitosis, and muscle differentiation, while IGF1 modulated IGF/PI3K signalling, metabolic alteration, and matrix structure. In addition, potential molecular markers were similarly modulated by both treatments. Muscle-miRNAs (miR-1, -133, -206 and -499) were up-regulated especially in AA samples, and we identified molecular networks with omics integration. Two pairs of genes and miRNAs showed high level of relationship, and involvement in myogenesis and muscle growth: marcksb and miR-29b in AA, and mmp14b and miR-338-5p in IGF1. Our work helps to elucidate fish muscle physiology and metabolism, highlights potential molecular markers, and creates perspective for improvements in aquaculture and in vitro meat production.

2022-01-26 | GSE192681 | GEO

Amino acids and IGF1 regulation of fish muscle growth revealed by transcriptome and microRNAome integrative analyses of pacu (Piaractus mesopotamicus) myotubes [miRNA-seq]

2022-01-26 | GSE192682 | GEO

Piaractus mesopotamicus

Project description:Piaractus mesopotamicus liver transcriptome

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Piaractus mesopotamicus

Project description:Piaractus mesopotamicus Transcriptome or Gene expression

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Piaractus mesopotamicus

Project description:Piaractus mesopotamicus Genome sequencing and assembly

| PRJNA754035 | ENA

Integrative microRNAome analysis of muscle tissue of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu) and the hybrid, tambacu, based on next-generation sequencing data.

Project description:Muscle miNRA analysis over two parental and the hybrid genotype

2021-03-04 | GSE147532 | GEO

Gut microbiome from Piaractus mesopotamicus

Project description:Gut microbiome from Piaractus mesopotamicus Metagenome

| PRJNA482836 | ENA

Prolonged fasting/refeeding modifies proteome profile and parvalbumin expression in the fast-twitch muscle of pacu (Piaractus mesopotamicus)

Project description:Skeletal muscle in fish presents a high plasticity controlled by a dynamic balance between anabolic and catabolic signaling pathways. Decreased food availability can inhibit muscle growth and trigger muscle catabolism pathways, thu promoting muscle atrophy. In contrast, anabolism may be favored during restoration of food supply, promoting the muscle growth. Considering this, we analyzed fast-twitch muscle of juvenile Piaractus mesopotamicus (pacu) submitted to a prolonged fasting (30 days) and refeeding (up to 30 days) using shotgun proteomics and gene expression analysis. The relative rate of weight and length increase, as well as the expression of mafbx and igf -1 genes, suggest that prolonged fasting caused muscle atrophy and that 30 days of refeeding led to partial compensatory growth. Shotgun proteomics analysis identified 99 proteins after fasting and 71 proteins after refeeding periods, of which 23 and 17 were differentially expressed after fasting and after 30 days of refeeding, respectively. Most of these differentially expressed proteins were related to cytoskeleton, muscle contraction and muscle metabolism. Among these, parvalbumin (PVALB), a calcium-binding protein and food allergen, was selected for further RT-qPCR analysis, which showed that pvalb mRNA was not changed after 30 days of fasting and 30 days of refeeding, but it was downregulated after 6h and 24h of refeeding. This suggests a post-transcriptional regulation of PVALB in fish muscle. In conclusion, our results suggest that muscle atrophy and partial compensatory growth caused by prolonged fasting and refeeding affected the muscle proteome and PVALB expression. Our results can contribute to the understanding of muscle anabolic and catabolic pathways in response to changes in food availability.

2019-11-28 | PXD014232 | Pride

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