How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.

异源四倍体中的两个亚基因组如何通过结构和表达进化来适应共存和协调需要进行广泛的研究。在本研究中，我们报告了异源四倍体鲤鱼的基因组组装的改进、异源四倍体金鱼的更新的基因组注释以及类祖二倍体 Puntius tetrazona和外群二倍体Paracanthobrama guichenoti的染色体规模组装。异源四倍体的平行亚基因组结构进化具有染色体组成相当、蛋白质同一性较高、转座子分歧和含量相似、同源交换、同线性水平较好、序列补偿较强、纯化选择对称等特点。此外，我们观察了同种异体四倍体中的亚基因组表达分歧过程，包括亚基因组间/亚基因组内转拼事件、表达优势、表达水平降低、剂量补偿、更强的表达相关性、动态功能化和差异表达的平衡。假设异源四倍体中不同祖细胞引入的潜在疾病可以通过增加结构同质性和执行多功能表达过程来缓解。对三种常见鲤鱼品系进行重新测序揭示了两种主要生态型，并发现了与生长和存活率相关的候选基因。