The phased pan-genome of tetraploid European potato

Hequan Sun, Sergio Tusso, Craig I. Dent, Manish Goel, Raúl Y. Wijfjes, Lisa C. Baus, Xiao Dong, José A. Campoy, Ana Kurdadze, Birgit Walkemeier, Christine Sänger, Bruno Huettel, Ronald C. B. Hutten, Herman J. van Eck, Klaus J. Dehmer and Korbinian Schneeberger ()
Additional contact information
Hequan Sun: Xi’an Jiaotong University
Sergio Tusso: LMU Munich
Craig I. Dent: Max Planck Institute for Plant Breeding Research
Manish Goel: LMU Munich
Raúl Y. Wijfjes: LMU Munich
Lisa C. Baus: LMU Munich
Xiao Dong: Max Planck Institute for Plant Breeding Research
José A. Campoy: Max Planck Institute for Plant Breeding Research
Ana Kurdadze: LMU Munich
Birgit Walkemeier: Max Planck Institute for Plant Breeding Research
Christine Sänger: Max Planck Institute for Plant Breeding Research
Bruno Huettel: Max Planck Institute for Plant Breeding Research
Ronald C. B. Hutten: Wageningen University & Research
Herman J. van Eck: Wageningen University & Research
Klaus J. Dehmer: Heinrich-Heine University
Korbinian Schneeberger: LMU Munich

Nature, 2025, vol. 642, issue 8067, 389-397

Abstract: Abstract Potatoes were first brought to Europe in the sixteenth century1,2. Two hundred years later, one of the species had become one of the most important food sources across the entire continent and, later, even the entire world3. However, its highly heterozygous, autotetraploid genome has complicated its improvement since then4–7. Here we present the pan-genome of European potatoes generated from phased genome assemblies of ten historical potato cultivars, which includes approximately 85% of all haplotypes segregating in Europe. Sequence diversity between the haplotypes was extremely high (for example, 20× higher than in humans), owing to numerous introgressions from wild potato species. By contrast, haplotype diversity was very low, in agreement with the population bottlenecks caused by domestication and transition to Europe. To illustrate a practical application of the pan-genome, we converted it into a haplotype graph and used it to generate phased, megabase-scale pseudo-genome assemblies of commercial potatoes (including the famous French fries potato ‘Russet Burbank’) using cost-efficient short reads only. In summary, we present a nearly complete pan-genome of autotetraploid European potato, we describe extraordinarily high sequence diversity in a domesticated crop, and we outline how this resource might be used to accelerate genomics-assisted breeding and research.

Date: 2025
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DOI: 10.1038/s41586-025-08843-0

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