ArticleGigaScience2025
Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
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3 authors.
Funding
Abstract
backgroundKoi 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.
resultsWe 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.
conclusionsOur 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.
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