# Genomic consequences of residual recombination in a hybrid apomictic hickory complex

## TL;DR

This study explores how rare sexual events in asexual hickory plants affect their genomes, revealing that recombination helps expose harmful mutations and supports clonality.

## Contribution

The study provides a genomic snapshot of residual sex in apomictic hickories and its role in mutation load and clonal maintenance.

## Key findings

- Apomictic species show genomic signatures of clonality, including loss of heterozygosity from rare sexual events.
- Apomictic adults have lower realized mutation loads despite more heterozygous deleterious variants.
- Recombination in embryos exposes harmful mutations to selection, aiding clonal maintenance.

## 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.

Apomixis allows plants to reproduce clonally, yet it is unclear how rare sexual events shape their genomes. This study shows that residual sex in apomictic hickories causes recombination-driven loss of heterozygosity that exposes harmful mutations to selection and helps maintain clonality.