2025/01/01 by Chao Bian, Rujingwen Huan, Qiong Shi · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Medicine · #Chromosomal and Genetic Variations #Genomics and Phylogenetic Studies #Telomeres, Telomerase, and Senescence
paper · pdf · doi:10.1093/gigascience/giaf073
openalex publication_date 2025/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
BACKGROUND: Koi carp, a variant of the common carp, is one of the most popular ornamental fish. Its genomic resources can help us better understand chromosome evolution and color phenotypes in cyprinid fish. RESULTS: We constructed telomere-to-telomere chromosome-level genome assemblies for 2 koi carp variants (black and golden) by integrating MGI, PacBio HiFi, ONT, and Hi-C sequencing technologies. Haplotypic genomes comprised 50 chromosomes with 100 and 99 telomeres, respectively, with BUSCO results showing at least 98.8% completeness. We annotated a total of 55,023 and 54,569 protein-coding genes for black and golden koi carps, respectively, with over 96% assigned functional roles. Repetitive sequences occupy an estimated 636 Mb (41%) of the genomes. With phylogenetic analysis, we predict the koi carp variants to have split 5.3 million years ago, and we constructed an ancient karyotype of 25 ancestral chromosomes to reveal 9 major chromosomal rearrangements. CONCLUSIONS: Our study offers genome assemblies capable of predicting an ancient karyotype of Cypriniformes, with genomic resources available for in-depth investigations into diverse skin coloration in koi and other cypriniforms.