Leibniz-Institute of Freshwater Ecology and Inland Fisheries-IGB (Forschungsverbund Berlin), Müggelseedamm 301, D-12587, Berlin, Germany.
University of Würzburg, Developmental Biochemistry, Biocenter, D-97074, Würzburg, Germany.
Nat Commun. 2022 Jul 14;13(1):4092. doi: 10.1038/s41467-022-31515-w.
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.
理解多倍体的基因组进化需要对其高度相似的亚基因组和单倍型进行剖析。迄今为止，多倍体动物基因组组装将同源染色体限制在“折叠”的表示形式中。在这里，我们对无性繁殖的普鲁士鲤鱼进行了测序，它是金鱼的近亲，并提供了一个六倍体动物的单倍型分辨率的染色体尺度组装。通过与两个祖先的二倍体鲤鱼以及异源四倍体金鱼和鲤鱼的 150 条染色体的全基因组比较，揭示了其基因组的基因组结构、系统发育和基因组复制历史。它由 25 个同源的、同系的染色体群组成，并通过最近对异源四倍体祖先的自体加倍而进化而来。我们表明，在个体基因水平上，全异源亚基因组的去多倍化以平衡的方式发生。对高度保守的硬骨鱼基因集的分析揭示了一个祖先染色体组在重复基因丢失中的亚基因组优势。
