Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Dadong Dai, Chuanshuai Xie, Yayi Zhou, Dexin Bo, Shurong Zhang, Shengqiang Mao, Yucheng Liao, Simeng Cui, Zhaolu Zhu, Xueyu Wang, Fanling Li, Donghai Peng (), Jinshui Zheng () and Ming Sun ()
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Dadong Dai: Huazhong Agricultural University
Chuanshuai Xie: Huazhong Agricultural University
Yayi Zhou: Huazhong Agricultural University
Dexin Bo: Huazhong Agricultural University
Shurong Zhang: Huazhong Agricultural University
Shengqiang Mao: Huazhong Agricultural University
Yucheng Liao: Huazhong Agricultural University
Simeng Cui: Huazhong Agricultural University
Zhaolu Zhu: Huazhong Agricultural University
Xueyu Wang: Huazhong Agricultural University
Fanling Li: Huazhong Agricultural University
Donghai Peng: Huazhong Agricultural University
Jinshui Zheng: Huazhong Agricultural University
Ming Sun: Huazhong Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-42700-w

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