Dataset Information

Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae.

ABSTRACT: Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5?Mb with the contig N50 of 1.80?Mb and the scaffold N50 of 5.05?Mb. The assembly covers 98.9% of the estimated genome size (655?Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family.

SUBMITTER: Zhang DC

PROVIDER: S-EPMC6805935 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae.

Zhang Dian-Chang DC Guo Liang L Guo Hua-Yang HY Zhu Ke-Cheng KC Li Shang-Qi SQ Zhang Yan Y Zhang Nan N Liu Bao-Suo BS Jiang Shi-Gui SG Li Jiong-Tang JT

Scientific data 20191022 1

Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 M ...[more]

PMID: 31641137

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Project description:Long chain acyl-coA synthase (acsl) family genes activate the conversion of long chain fatty acids into acyl-coA to regulate fatty acid metabolism. However, the evolutionary characteristics, tissue expression and nutritional regulation of the acsl gene family are poorly understood in fish. The present study investigated the molecular characterization, tissue expression and nutritional regulation of the acsl gene family in golden pompano (Trachinotus ovatus). The results showed that the coding regions of acsl1, acsl3, acsl4, acsl5 and acsl6 cDNA were 2091 bp, 2142 bp, 2136 bp, 1977 bp and 2007 bp, encoding 697, 714, 712, 659 and 669 amino acids, respectively. Five acsl isoforms divided into two branches, namely, acsl1, acsl5 and acsl6, as well as acsl3 and acsl4. The tissue expression distribution of acsl genes showed that acsl1 and acsl3 are widely expressed in the detected tissues, while acsl4, acsl5 and acsl6 are mainly expressed in the brain. Compared to the fish fed with lard oil diets, the fish fed with soybean oil exhibited high muscular C18 PUFA contents and acsl1 and acsl3 mRNA levels, as well as low muscular SFA contents and acsl4 mRNA levels. High muscular n-3 LC-PUFA contents, and acsl3, acsl4 and acsl6 mRNA levels were observed in the fish fed with fish oil diets compared with those of fish fed with lard oil or soybean oil diets. High n-3 LC-PUFA levels and DHA contents, as well as the acsl3, acsl4 and acsl6 mRNA levels were exhibited in the muscle of fish fed diets with high dietary n-3 LC-PUFA levels. Additionally, the muscular acsl3, acsl4 and acsl6 mRNA expression levels, n-3 LC-PUFA and DHA levels were significantly up-regulated by the increase of dietary DHA proportions. Collectively, the positive relationship among dietary fatty acids, muscular fatty acids and acsl mRNA, indicated that T. ovatus Acsl1 and Acsl3 are beneficial for the C18 PUFA enrichment, and Acsl3, Acsl4 and Acsl6 are for n-3 LC-PUFA and DHA enrichment. The acquisition of fish Acsl potential function in the present study will play the foundation for ameliorating the fatty acids nutrition in farmed fish products.

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Dataset Information

Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae.

Publications

Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae.

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