Telomere-to-telomere gapless genome assembly of Siniperca scherzeri

The mandarin fish (Siniperca scherzeri), renowned as the “freshwater grouper”, has emerged as a commercially significant aquaculture species in China due to its superior flesh quality, disease resistance, and domestication adaptability. With the rapid development of bioinformatics, higher standards of genome analysis are now required compared to previous reference genomes. In this study, we integrated PacBio HiFi long-read sequencing, Oxford Nanopore Technologies ultralong-read sequencing, and Hi-C chromatin conformation capture to assemble a near-complete telomere-to-telomere genome. The gapless assembly spans 24 chromosomes, with telomeric repeats detected at both ends of 20 chromosomes and at only one end of the remaining four chromosomes. BUSCO evaluation against the Actinopterygii database (actinopterygii_odb10) revealed 98.7% genome completeness. Alignment analyses using minimap2 demonstrated >97% mapping rates for ONT ultralong reads, PacBio HiFi reads, and Hi-C data against the assembled genome. We annotated 23,296 protein-coding genes, establishing a crucial genomic resource for elucidating the species’ evolutionary biology and advancing molecular breeding strategies.