Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers
Crop wild relatives are used to improve cultivated plants and precise tracking of genetic introgression requires high-quality genome assemblies. Here we present de novo genome assemblies of two wild tomato species - the broadly stress-resistant Solanum pennellii (LA0716) and the salt-resistant Solanum cheesmaniae (LA1039). The improved S. pennellii genome adds 146 Mbp to the twelve chromosomes compared with the original reference. The alignment of the new assemblies with multiple gold-standard assemblies identified shared and species-specific structural variants. Analysis of repeat content demonstrates independent explosions of Tekay retrotransposons in S. pennellii and S. peruvianum. Genome sequencing of 709 recombinant plants derived from male and female backcrosses of three different hybrids reveals higher crossover rate in female meiosis. Conserved female-enhanced recombination regions were discovered and coldspots were attributed to megabase-scale inversions and insertion-deletion polymorphisms. Our S. pennellii and S. cheesmaniae genome assemblies reveal how repeat content diverged in nature and during breeding, and uncovers how both reproductive gender and structural variants dictate recombination landscapes in tomato hybrids.
Authors
- Saleh Alseekh (ORCID: https://orcid.org/0000-0003-2067-5235)
- Björn Usadel (ORCID: https://orcid.org/0000-0003-0921-8041)
- Charles J. Underwood (ORCID: https://orcid.org/0000-0001-5730-6279)
- Tamara Susanto (ORCID: https://orcid.org/0000-0002-4785-1166)
- Roven Rommel Fuentes (ORCID: https://orcid.org/0009-0002-8512-619X)
- Elias Primetis (ORCID: https://orcid.org/0000-0003-0502-2447)
- Zahra Zangishei (ORCID: https://orcid.org/0000-0003-3882-8164)
- Qichao Lian (ORCID: https://orcid.org/0000-0003-0737-8332)
- Yazhong Wang (ORCID: https://orcid.org/0000-0001-8150-7230)
- Sieglinde Effgen
- Willem M. J. van Rengs
- Bruno Hüettel (ORCID: https://orcid.org/0000-0001-7165-1714)
- Joiselle Blanche Fernandes (ORCID: https://orcid.org/0000-0003-2540-2439)
Institutions
- South China Agricultural University (CN)
- Radboud University Nijmegen (NL)
- Forschungszentrum Jülich (DE)
- Radboud University Medical Center (NL)
- Center of Plant Systems Biology and Biotechnology (BG)
- Max Planck Institute of Molecular Plant Physiology (DE)
- Radboud Institute for Molecular Life Sciences (NL)
- Institute of Genetics and Developmental Biology (CN)
- Cluster of Excellence on Plant Sciences (DE)
- KeyGene (Netherlands) (NL)
- Max Planck Institute for Plant Breeding Research (DE)
- Heinrich Heine University Düsseldorf (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-06-28
- DOI
- https://doi.org/10.1038/s41467-026-74784-5
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 0.00