ArticleNature genetics2022
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
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Who cites it
141 citing papers in PubMed.
- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Allelic expression and subgenome bias influence plant height in cultivated hybrid sugarcane.aBIOTECH · 2026Article
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Genomic constraint and hypervariability correlate with fitness effects in elite tetraploid potato breeding material.PLoS genetics · 2026Article
- LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq.Plant methods · 2026Article
- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Evolutionary tuning of a biosynthetic gene cluster drives furanocoumarin accumulation and diversification.Nature communications · 2026Article
- Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance.The plant genome · 2026Article
- A chromosome-level genome assembly of Solanum brevicaule (PI 473011) Y1-5, a wild potato relative with robust resistance to potato cyst nematodes.The plant genome · 2026Article
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Identification ofPlants (Basel, Switzerland) · 2026Article
- A rare glycoalkaloid biosynthetic pathway from wild potato unlocks genetic routes to Colorado potato beetle resistance.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Review
- Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding.The plant genome · 2026Article
- BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing.aBIOTECH · 2026Article
- Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.Genome biology · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- The Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Nature communications · 2026Article
81 more citing papers are in PubMed but not listed here.
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar 'Otava' based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.
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