Supporting data for "Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes"

Koi carp (<i>Cyprinus carpio</i> var. koi) has served as an important model for studying fish pigmentation, due to its precious variability in skin color. It is also an excellent model to study chromosome changes after undergoing whole genome duplication. <br>We constructed two telomere-to-telomere chromosome-level genome assemblies for black and golden koi carp variants by integration of MGI, PacBio HiFi, ONT, and Hi-C sequencing technologies. Haplotypic genomes of the black and golden koi carps covered 50 chromosomes with 100 and 99 telomeres, respectively. BUSCO results validated 98.9% and 98.8% completeness of both genomes. A total of 55,023 and 54,569 protein-coding genes were respectively annotated in the assembled genomes. Of them, 96.1% and 97.1% were assigned with functional roles. We also estimated that the black and golden koi carp genomes contain 636.2 Mb and 636.3 Mb of repetitive sequences, accounting for 40.6% and 40.9% of their whole genomes. Based on a phylogenetic analysis and divergence time estimation, we predicted that these two koi carps split from each other about 5.3 million years ago. By analyzing chromosome sequences of seven representative Cypriniformes species, we constructed an ancient karyotype of 25 ancestral chromosomes, which revealed nine major chromosomal rearrangements in the examined species. <br>These extremely high-quality data offer valuable genomics resources, which support to predict an ancient karyotype of Cypriniformes. Both T2T genome assemblies can also be used as good references for in-depth genetic and evolutionary investigations on diverse skin coloration in koi and other Cypriniformes species.