ArticleGenome biology2026
Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.
Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Remodeling of the tuberization-controlling FLOWERING LOCUS T genes from non-tuberizing ancestor to potato.The Plant journal : for cell and molecular biology · 2026Article
- Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.Genome biology · 2026Article
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9 authors.
Funding
Abstract
backgroundPotato (Solanum tuberosum) breeding is severely hindered by its highly heterozygous autotetraploid genome, where complex allelic interactions impede precise trait selection. Reconstructing complete haplotype-resolved assemblies is crucial for genome-assisted breeding. However, current assembly methods for autopolyploids often generate fragmented sequences, haplotype-switch errors, and gaps in complex regions such as centromeres.
resultsTo address these challenges, we develop PHap, a haplotype assembly pipeline tailored for autopolyploids, using only standard sequencing data, including long-reads and Hi-C. Applying PHap to the autotetraploid potato cultivar HuaShu4, we generate a haplotype-resolved, near telomere-to-telomere assembly of 3.12 Gb with an N50 of 32.7 Mb and 99.7% haplotype accuracy. Comparisons with alternative methods and existing assemblies highlight PHap's advantages in assembly quality and cost-effectiveness. Integration of transcriptomic and epigenomic data demonstrates that the genomic and methylation divergence across haplotypes drives substantial allelic expression differentiation. Time-course RNA-seq further reveals, for the first time, that 55% of genes exhibit divergent allelic expression, with dynamic shifts in dominant or suppressed alleles during tuber development. Additionally, our assembly resolves high-resolution haplotype-specific structures in centromeres and subtelomeres, as well as haplotype divergence of structural rearrangements. It also shows neocentromere formation via the expansion of megabase-scale satellite arrays.
conclusionsThese findings provide insights into the architecture of autopolyploid genomes and establish a foundation for genomics-assisted breeding of polyploid potatoes.
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