Abstract Pangasius nasutus (Bleeker, 1863), locally known as ‘Patin buah’, is a commercially valuable freshwater catfish native to Peninsular Malaysia. Unlike the commonly farmed pangasiids Pangasianodon hypophtalmus , Pangasius djambal and P. sanitwongsei , P. nasutus is prized for its firmer texture, lower fat content, and distinctive flavour, making it a premium aquaculture species. Despite its ecological and economic importance, wild populations have declined significantly owing to overfishing and habitat modification, with limited genomic information available to date. Here, we present the first genome of P. nasutus generated using a hybrid Illumina-PacBio sequencing approach. The assembled genome spans 822.3 Mb with a scaffold N50 of 12.9 Mb and 98.6% BUSCO completeness, representing one of the most complete assemblies within the Pangasiidae. Gene annotation predicted 25,987 gene models, of which 89.1% were classified as complete based on BUSCO assessment. Comparative genomic analysis with P. djambal , P. gigas , and P. hypophtalmus revealed a large conserved orthogroup core alongside 198 unique orthogroups specific to P. nasutus . Functional enrichment of these species-specific genes indicated significant overrepresentation of chemosensory perception, G-protein-coupled receptor signalling, immune system processes, and reproductive and developmental pathways, suggesting genomic innovations linked to feeding ecology, environmental adaptation, and reproductive synchronisation in variable riverine habitats. Phylogenomic reconstruction based on single-copy orthologs confirmed the deep divergence between Pangasianodon and Pangasius , with P. nasutus forming a robust sister clade to P. conchophilus . This topology is congruent with previous mitogenomic studies of pangasiids, reinforcing the evolutionary coherence and taxonomic validity of the genus Pangasius . Overall, the genome of P. nasutus provides a foundational resource for functional, comparative, and conservation genomics of Malaysian pangasiids. It offers critical insights into the evolutionary history and adaptive diversification of the family Pangasiidae and lays the groundwork for future breeding, management, and genomic monitoring initiatives for native freshwater fishes.
Abdul-Halim et al. (Fri,) studied this question.