Gap-free telomere-to-telomere haplotypes assembly of the hybrid grouper 'Yushuban' (Cromileptes altivelis ♀ x Epinephelus fuscoguttatus ♂)

The hybrid grouper 'Yushuban' (Cromileptes altivelis ♀ x Epinephelus fuscoguttatus ♂) has shown promising performance in aquaculture trials, yet no complete reference genome has been available for this hybrid. We generated two gapless, telomere-to-telomere (T2T) haplotype-resolved genome assemblies of a single individual by integrating short-read, PacBio HiFi, Oxford Nanopore ultralong-read and Hi-C data. The maternal (Yushu_Calti_1.0) and paternal (Yushu_Efusc_1.0) haplotypes are 1,077.33 Mb and 1,083.36 Mb in length, with N50 values of 45.46 Mb and 45.55 Mb, respectively. Across all platforms, over 99.4% of reads mapped to each assembly, and Merqury-based quality values reached 57.7413 and 59.2068 (PacBio). BUSCO recovered 99.78% and 99.75% of complete core genes. We predicted 27,248 and 27,566 protein-coding genes, of which 98.52% and 99.23% were functionally annotated, and annotated telomeric motifs and repetitive elements (46.12% and 47.18% of each genome). These assemblies fill a gap in grouper genomic resources and provide a foundation for genetic dissection, parental genome comparison and molecular breeding of this hybrid.