biostudies-literatureUnknown6(9)Wang YTriploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexuaNature ecology & evolution1354-1366https://www.ebi.ac.uk/biostudies/studies/S-EPMC9439954biostudies-literatureComparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish.PMC9439954Zhu CLZhang QQMiao LJFu BDZhou BTBai MZYu PQiu QWu BWang KLu WJDing MJian JBFang XDGan RHChen YWang WWang ZWZheng JMWang YZhang CHe WMHu MLZhang YPZhou LXu MFeng CGTian LTGui JFYang HMYin ZGao QYang WLu MPeng FLi ZZhang XJTong JFLi XYXu WJTong JGYang YLZhao ZCXu JYfalseComparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish.Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexua2022-01-01T00:00:00Z2022 Sep2026-05-10T05:13:59.795Z2025-02-19T04:03:25.717ZS-EPMC94399543581782710.1038/s41559-022-01813-z