Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.

Amphibian Research Center Hiroshima University Higashi Hiroshima 739 8526 Japan

Czech University of Life Sciences Prague Prague Czech Republic

Leibniz Institute of Freshwater Ecology and Inland Fisheries IGB Müggelseedamm 301 D 12587 Berlin Germany

Research Department for Limnology Mondsee University of Innsbruck A 5310 Mondsee Austria

University of Würzburg Developmental Biochemistry Biocenter D 97074 Würzburg Germany

Xiphophorus Genetic Stock Center Texas State University San Marcos TX 78666 USA

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Nat Commun. 2022 Aug 8;13(1):4638. doi: 10.1038/s41467-022-32470-2. PubMed

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Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction

Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution