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A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli.

ABSTRACT: The darkbarbel catfish (Pelteobagrus vachelli), an economically important aquaculture species in China, is extensively employed in hybrid yellow catfish production due to its superior growth rate. However, information on its genome has been limited, constraining further genetic studies and breeding programs. Leveraging the power of PacBio long-read sequencing and Hi-C technologies, we present a high-quality, chromosome-level genome assembly for the darkbarbel catfish. The resulting assembly spans 692.10 Mb, with an impressive 99.9% distribution over 26 chromosomes. The contig N50 and scaffold N50 are 13.30 Mb and 27.55 Mb, respectively. The genome is predicted to contain 22,109 protein-coding genes, with 96.1% having functional annotations. Repeat elements account for approximately 35.79% of the genomic landscape. The completeness of darkbarbel catfish genome assembly is highlighted by a BUSCO score of 99.07%. This high-quality genome assembly provides a critical resource for future hybrid catfish breeding, comparative genomics, and evolutionary studies in catfish and other related species.

SUBMITTER: Gong G

PROVIDER: S-EPMC10491679 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli.

Gong Gaorui G Ke Wensi W Liao Qian Q Xiong Yang Y Hu Jingqi J Mei Jie J

Scientific data 20230908 1

The darkbarbel catfish (Pelteobagrus vachelli), an economically important aquaculture species in China, is extensively employed in hybrid yellow catfish production due to its superior growth rate. However, information on its genome has been limited, constraining further genetic studies and breeding programs. Leveraging the power of PacBio long-read sequencing and Hi-C technologies, we present a high-quality, chromosome-level genome assembly for the darkbarbel catfish. The resulting assembly span ...[more]

PMID: 37684295

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Project description:Background: Yellow catfish (Pelteobagrus fulvidraco) is one of the important aquaculture species in China. In recent years, due to the high breeding density, the increasing frequency of feeding, and the excessive addition of feed fat, the excessive deposition of body fat in cultured yellow catfish has become more frequent. MicroRNAs (miRNAs) are an important gene expression regulatory signal molecule that regulates liver fat synthesis and transport and play an important role in fat deposition. However, there is a little research on the mechanism of fatty liver caused by excessive deposition of liver fat. Results: After 60 days of high-fat stress, the growth and feed conversion rate of hybrid yellow catfish (Pelteobagrus fuIvidraco♀×P. vachelli♂) were significantly inhibited, and hepatosomatic index, viscerosomatic index, hepatic triglyceride and cholesterol, and red lipid droplets in liver tissues were increased. Through high-throughput sequencing, we constructed miRNA libraries of high-fat stress at 60d, identified 346 conserved miRNAs and 410 novel miRNAs, among which 13 differentially expressed miRNAs were screened between high-fat diet group and normal-fat diet group. Also, we constructed mRNA transcriptome libraries after high-fat stress. Potential target genes for differentially expressed miRNAs were identified by bioinformatics analysis. Seven miRNA-mRNA pairs were screened. The expression of differential miRNA and mRNA and potential binding sites were analyzed by qRT-PCR and dual luciferase assay. Hybrid yellow catfish could promote the oxidative degradation of liver glucose, reduce fatty acid peroxidation, regulate antioxidant enzyme activity and response of immune and inflammatory to relieve fat deposition and liver stress. Conclusions: The disorders of fat metabolism in liver not only result in feed wastage, increase metabolic burden of yellow catfish, but also cause immune function damage, resulting in a variety of nutritional diseases. The development of this study is to understand the molecular mechanism of hepatic fat deposition in yellow catfish. It has important biological significance for improving protection of liver against stress and healthy culture.

Dataset Information

A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli.

Publications

A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli.

Similar Datasets

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