Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

  1. Wen-Biao Jiao
  2. Kristin Krause
  3. Jose Campoy
  4. Manish Goel
  5. Kat Folz-Donahue
  6. Christian Kukat
  7. Bruno Huettel
  8. Korbinian Schneeberger
Plant and Animal Genome Conference (PAG) 2022

Year of publication: 2022

Type: Conference paper


Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. We have developed an effective method to separately assemble the four highly divergent haplotypes of cultivated potato genomes, by coupling single-cell sequencing of a few hundred pollen genomes with high-fidelity long reads. In this presentation, I will explain how we generated a 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the tetraploid cultivar ‘Otava’. With this assembly, we found footprints of inbreeding leading to around 50% of the genomic regions being identical-by-descent, while there are strong haplotype divergence in the remaining regions. I will also show how the generation of such a high-quality genome assembly can help analyze the functional organization of the tetraploid genome.