The formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by parthenogenesis and allopolyploidy, show a widespread geographical distribution and extensive agricultural destruction. Here, we generated 4 unzipped polyploid RKN genomes and identified a putative novel alternative telomeric element. Then we reconstructed 4 chromosome-level assemblies and resolved their genome structures as AAB for triploid and AABB for tetraploid. The phylogeny of subgenomes revealed polyploid RKN origin patterns as hybridization between haploid and unreduced gametes. We also observed extensive chromosomal fusions and homologous gene expression decrease after polyploidization, which might offset the disadvantages of clonal reproduction and increase fitness in polyploid RKNs. Our results reveal a rare pathway of polyploidization in parthenogenic polyploid animals and provide a large number of high-precision genetic resources that could be used for RKN prevention and control.

克隆繁殖动物中多倍化的形成和后果仍然很大程度上未知。I 类根结线虫 (RKN) 以单性生殖和异源多倍体为特征，表现出广泛的地理分布和广泛的农业破坏。在这里，我们生成了 4 个解压缩的多倍体 RKN 基因组，并鉴定了一个假定的新型替代端粒元件。然后我们重建了4个染色体水平的组装体，并将其基因组结构解析为三倍体的AAB和四倍体的AABB。亚基因组的系统发育揭示了多倍体 RKN 起源模式为单倍体和未减数配子之间的杂交。我们还观察到多倍化后广泛的染色体融合和同源基因表达减少，这可能抵消克隆繁殖的缺点并增加多倍体 RKN 的适应性。我们的研究结果揭示了单性多倍体动物中罕见的多倍体化途径，为RKN防治提供了大量高精度的遗传资源。