A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus).
Genomics, 2021/09;113(5):3349-3356.
Gao Z[1], You X[1], Zhang X[2], Chen J[1], Xu T[2], Huang Y[2], Lin X[3], Xu J[2], Bian C[1], Shi Q[4]
Affiliations
PMID: 34343676DOI: 10.1016/j.ygeno.2021.07.026
Impact factor: 4.31
Abstract
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.
Keywords: Chromosome-scale genome assembly; Fatty acid binding protein 1; Striped catfish (Pangasianodon hypophthalmus); Whole genome sequencing
MeSH terms
Animals; Catfishes; Chromosomes; Genome; High-Throughput Nucleotide Sequencing; Repetitive Sequences, Nucleic Acid
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