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; Ming Sun

doi:10.1038/s41467-023-42700-w

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

Nat Commun. 2023 Nov 7;14(1):7156. doi: 10.1038/s41467-023-42700-w.

Authors

Dadong Dai^#^{1

2}, Chuanshuai Xie^#^{1

2}, Yayi Zhou^{1

3}, Dexin Bo^{1

3}, Shurong Zhang^{1

2}, Shengqiang Mao^{1

3}, Yucheng Liao^{1

3}, Simeng Cui^{1

2}, Zhaolu Zhu^{1

3}, Xueyu Wang^{1

2}, Fanling Li^{1

2}, Donghai Peng^{4

5}, Jinshui Zheng^{6

7}, Ming Sun^{8

9}

Affiliations

¹ State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
² College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
³ Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
⁴ State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. donghaipeng@mail.hzau.edu.cn.
⁵ College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. donghaipeng@mail.hzau.edu.cn.
⁶ State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. jszheng@mail.hzau.edu.cn.
⁷ Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. jszheng@mail.hzau.edu.cn.
⁸ State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. m98sun@mail.hzau.edu.cn.
⁹ College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. m98sun@mail.hzau.edu.cn.

^# Contributed equally.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromosomes
Germ Cells
Hybridization, Genetic
Nematoda* / genetics
Polyploidy*
Triploidy