Abstract
Apomixis, a form of clonal asexual reproduction in plants, is often accompanied by residual sex, yet its genomic consequences remain poorly understood. Here, we assembled a haplotype-resolved genome of Carya hunanensis and analyzed whole-genome resequencing data from 195 adults and 180 mature embryos across four hickory species, representing a hybrid apomictic complex with both sexual and asexual lineages. We find apomictic species exhibited genomic signatures of clonality, notably loss of heterozygosity (LOH), suggesting recombination induced by rare sexual events. Despite harboring more heterozygous deleterious variants, apomictic adults showed lower realized mutation loads, particularly in hybrid C. hunanensis, whose apomictic haplotype disproportionately carried deleterious alleles. Remarkably, rare embryos from apomicts underwent recombination-mediated LOH, exposing deleterious mutations to selection. These findings reveal the genetic cost of residual sex, while also indicating its role in generating novel genotypes, supported by close relatedness among adult apomicts. Our study provides a unique genomic snapshot of how residual sex and recombination mitigate mutation accumulation and potentially facilitate clonal maintenance in natural asexual systems.
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Data availability
The raw sequence data reported in this paper have been deposited in the National Genomics Data Center (NGDC; https://ngdc.cncb.ac.cn) under the accession number PRJCA033579 and in GenBank under accession number PRJNA356989. The final genome assembly and genome annotation files are available at http://cmb.bnu.edu.cn/juglans. All other data supporting the findings of this study are present in the paper and/or its Supplementary Materials. Source data are provided with this paper.
Code availability
The custom scripts used for the primary loss of heterozygosity (LOH) analyses are available at https://github.com/Hickory01/Apomixis-in-Hickory-Species.git.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (32400311 to W.P.Z.), the “111” Program of Introducing Talents of Discipline to Universities (B13008 to D.Y.Z.), the Fundamental Research Funds for the Central Universities (to D.Y.Z.), China Postdoctoral Science Foundation (2023M733549 to W.P.Z.) and the Chinese Academy of Sciences (CAS) Scholarship Program (to W.P.Z.). We thank Dr. Shou-Jie Li (South China Botanical Garden, Chinese Academy of Sciences), Dr. Yu Cao, Dr. Yang Yang and Dr. Rui-Min Yu (Beijing Normal University), Shi-Bin Jiao, You-Liang Xiang (Guizhou Normal University), Zhi-Quan Liu (Hangzhou Normal University), Kai-Bing Liu, and Zhi-Xiang Chen for their invaluable assistance with sample collection. We also thank Dr. Nan Wang (Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences) and Dr. Huiqin Yi (Stockholm University) for their insightful comments on the analysis.
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W.N.B., D.Y.Z., M.L., and M.K. conceived and supervised the project. W.P.Z. collected the materials and performed the main analyses. S.G. provided constructive suggestions regarding the loss of heterozygosity (LOH) analysis. X.X.P. conducted the LOH detection analysis. M.K. provided guidance on the analytical workflow for genetic load analysis. W.P.Z. and W.N.B. drafted the manuscript. W.N.B., M.L., S.G., and D.Y.Z. revised and proofread the manuscript. All authors approved the final version.
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Zhang, WP., Glémin, S., Pang, XX. et al. Genomic consequences of residual recombination in a hybrid apomictic hickory complex. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68867-6
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DOI: https://doi.org/10.1038/s41467-026-68867-6
