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Background: Hong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species. Results: The first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes. Conclusions: This study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish. [ABSTRACT FROM AUTHOR]

Sillago sihama is a tropical fish from India to the western Pacific. It is widely distributed in the coastal waters of southern China and is one of the most important economic fish species. The factor inhibiting hypoxia inducible factor-1 (fih-1) is a key factor in the hypoxia signal pathway. It plays an important role in the hypoxia adaptation in fishes. The fih-1 gene of S. sihama was cloned, and its cDNA sequence was 1280 bp, including an open reading frame of 1065 bp, encoding 353 amino. The structure prediction found that there was a JmjC conserved domain. Multi-sequence alignment and cluster analysis based on fih-1 amino acid sequences showed that the S. sihama was closely related to Larimichthys crocea and Lates calcarifer, bur farther to mammals, amphibians, and birds. The fih-1 was strongly expressed in the testis, ovary, and muscle, followed by the gill, heart and liver, but weakly expressed in the brain. The expression of fih-1 gene in gill and heart increased significantly after 1-hour hypoxia stress, and it continued to increase significantly after 6 hours. After 4 hours of normal dissolved oxygen, the expression decreased significantly but it was still higher than the normal level (P<0.05). This study revealed that fih-1 gene plays an important role in the hypoxic signal conduction pathway and provides candidate genes for carrying out and explaining the genetic mechanism of S. sihama. [ABSTRACT FROM AUTHOR]