A telomere-to-telomere gap-free genome assembly of the striped catfish (Pangasianodon hypophthalmus)

The well-known striped catfish (Pangasianodon hypophthalmus), belonging to the order Siluriformes and the family Pangasiidae, has become an important freshwater economic fish species due to its outstanding growth performance, environmental adaptability and disease resistance. In this study, we reported the first telomere-to-telomere (T2T) gap-free genome assembly of striped catfish, generated by integrating MGI short-read, ONT ultra-long read, PacBio HiFi long read and Hi-C data. A total of 772.03 Mb genome sequences were successfully anchored onto 30 chromosomes, demonstrating exceptional contiguity with a high contig N50 of 26.47 Mb. A comprehensive annotation revealed precise structure of telomeric repeats and centromeric region within each chromosome. In the assembled genome, repetitive elements accounted for 39.53% (305.21 Mb), with DNA transposons (20.77%) as the predominant repeat type. A total of 24,596 protein-coding genes were predicted (BUSCO: 96.21%), and 99.22% of these genes were functionally annotated. Our combined results about identification of telomeric repeats and centromeric regions, BUSCO assessment (99.45%), mapping coverage (99.55%), and Clipping information for Revealing Assembly Quality (CRAQ: 99.62%) support the high quality of this genome assembly. These complete chromosomal sequences will serve as a valuable genetic resource for in-depth biological investigations, evolutionary studies, comparative genomics, and molecular breeding to improve economic value of the striped catfish.