Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes

ABSTRACT Airbreathing catfishes are a group of stenohaline freshwater fish that can withstand various environmental conditions and farming practices, including the ability to breathe atmospheric oxygen. This unique ability has allowed them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological conditions remain poorly understood. Here, we sequenced the genome of the African catfish Clarias gariepinus , one of the most commonly farmed clariids. By integrating different long reads sequencing technologies, we generated a chromosome-level assembly with high-resolution haplotypes, including the male-specific haplotype. The diploid assembly yielded 58 contigs spanning 969.72 Mb with a contig N50 of 33.71 Mb. We report 25,655 predicted protein-coding genes and 49.94% repetitive elements in the African catfish genome. Several gene families involved in ion transport, osmoregulation, oxidative stress response, and muscle metabolism were expanded or positively selected in clariids, suggesting a potential role in their transition to terrestrial life. The reported findings expand our understanding of the genomic mechanisms underpinning the resilience and adaptive mechanisms of C. gariepinus to adverse environments. These insights will serve as a valuable resource for future studies in elucidating these unique biological traits in related teleosts and leverage these insights for aquaculture improvement.