Spooner, D. M. et al. A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proc. Natl Acad. Sci. USA 102, 14694–14699 (2005).
Hawkes, J. G. Genetic poverty of the potato in Europe. In Proc. of the Conference: Broadening the Genetic Base of Crops (eds Zeven, A. C. & van Harten, A. M.) 19–27 (Centre for Agricultural Publishing and Documentation, Wageningen, Netherlands, 1979).
Gutaker, R. M. et al. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat. Ecol. Evol. 3, 10930–11101 (2019).
Hoopes, G. et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant 15, 520–536 (2022).
Mari, R. S. et al. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biol. 25, 26 (2024).
Sun, H. et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat. Genet. 54, 342–348 (2022).
Bao, Z. et al. Genome architecture and tetrasomic inheritance of autotetraploid potato. Mol. Plant 15, 1211–1226 (2022).
Devaux, A. et al. Global food security, contributions from sustainable potato agri-food systems. In The Potato Crop (eds Campos, H. & Ortiz, O.) 3–35 (Springer, 2020).
Liao, W. W. et al. A draft human pangenome reference. Nature 617, 312–324 (2023).
The 1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481–491 (2016).
Hawkes, J. G. The early history of the potato in Europe. Euphytica 70, 1–7 (1993).
Kloosterman, B. et al. Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495, 246–250 (2013).
Yoshida, K. et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife 2, e00731 (2013).
Hardigan, M. A. et al. Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. Proc. Natl Acad. Sci. USA 114, E9999–E10008 (2017).
Vos, P. G. et al. Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theor. Appl. Genet. 128, 2387–2401 (2015).
Glendinning, D. R. et al. Potato introductions and breeding up to the early 20th century. New Phytol. 94, 479–505 (1983).
Hutten, R. C. B. and van Berloo, R. Potato Pedigree Database. Wageningen University & Research https://www.plantbreeding.wur.nl/PotatoPedigree/ (accessed 2 July 2021).
van Berloo, R., Hutten, R. C. B., van Eck, H. J. & Visser, R. G. F. An online potato pedigree database resource. Potato Res. 50, 45–57 (2007).
Diekmann, K. et al. Diversity studies in genetic resources of Solanum spp. (section Petota) by comparative application of ISAP markers. Genet. Resour. Crop Evol. 64, 1937–1953 (2017).
Ríos, D., Devaux, A. & Ruiz de Galarreta, J. I. Ancient potato varieties of the Canary Islands: their history, diversity and origin of the potato in Europe. Potato Res. 67, 963–994 (2023).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Tang, D. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535–541 (2022).
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 1–27 (2020).
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).
Clot, C. R. et al. High-density linkage map constructed from a skim sequenced diploid potato population reveals transmission distortion and QTLs for tuber yield and pollen shed. Potato Res. 67, 139–163 (2023).
Leffler, E. M. et al. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol. 10, e1001388 (2012).
Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs with minigraph. Genome Biol. 21, 265 (2020).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Wu, Y. et al. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186, 2313–2328.e15 (2023).
Zhang, C. et al. Genome design of hybrid potato. Cell 184, 3873–3883.e12 (2021).
Zhou, Q. et al. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat. Genet. 52, 1018–1023 (2020).
Schrinner, S. D. et al. Haplotype threading: accurate polyploid phasing from long reads. Genome Biol. 21, 252 (2020).
Ebler, J. et al. Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat. Genet. 54, 518–525 (2022).
Du, Z.-Z., He, J. B. & Jiao, W. B. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biol. 25, 91 (2024).
Schneeberger, K. et al. Simultaneous alignment of short reads against multiple genomes. Genome Biol. 10, R98 (2009).
Gebhardt, C., Ballvora, A., Walkemeier, B., Oberhagemann, P. & Schüler, K. Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol. Breed. 13, 93–102 (2004).
D’hoop, B. B., Paulo, M. J., Mank, R. A., van Eck, H. J. & van Eeuwijk, F. A. Association mapping of quality traits in potato (Solanum tuberosum L.). Euphytica 161, 47–60 (2008).
Jansky, S. H. et al. Reinventing potato as a diploid inbred line-based crop. Crop Sci. 56, 1412–1422 (2016).
Sharma, S. K. et al. Linkage disequilibrium and evaluation of genome-wide association mapping models in tetraploid potato. G3 (Bethesda) 8, 3185–3202 (2018).
Smith, A. F. Potato: A Global History (Reaktion Books, 2011).
Bradshaw, J. & Ramsay, G. Utilisation of the commonwealth potato collection in potato breeding. Euphytica 120, 15–24 (2009).
Hickey, G. et al. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol. 21, 35 (2020).
Hickey, G. et al. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat. Biotechnol. 42, 663–673 (2023).
Bradbury, P. J. et al. The practical haplotype graph, a platform for storing and using pangenomes for imputation. Bioinformatics 38, 3698–3702 (2022).
Garrison, E. et al. Building pangenome graphs. Nat. Methods 21, 2008–2012 (2024).
Shang, L. et al. A super pan-genomic landscape of rice. Cell Res. 32, 878–896 (2022).
Cochetel, N. et al. A super-pangenome of the North American wild grape species. Genome Biol. 24, 290 (2023).
Guo, N. et al. A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. Plant Commun. 5, 100791 (2024).
European Commission. Common catalogue of varieties of agricultural plant species, version 27.01.2023. https://go.nature.com/3RArWL0 (2023).
Chen, Y. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7, gix120 (2018).
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Sun, H., Ding, J., Piednoël, M. & Schneeberger, K. findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics 34, 550–557 (2018).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Zhang, X., Zhang, S., Zhao, Q., Ming, R. & Tang, H. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat. Plants 5, 833–845 (2019).
Stanke, M., Schöffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62 (2006).
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).
Hoff, K. J., Lomsadze, A., Borodovsky, M. & Stanke, M. Whole-genome annotation with BRAKER. Methods Mol. Biol. 1962, 65–95 (2019).
Lomsadze, A., Burns, P. D. & Borodovsky, M. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Res. 42, e119 (2014).
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767–769 (2016).
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494–6506 (2005).
Iwata, H. & Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 40, e161 (2012).
Gotoh, O., Morita, M. & Nelson, D. R. Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment. BMC Bioinformatics 15, 189 (2014).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. 3, lqaa108 (2021).
Gabriel, L., Hoff, K. J., Brůna, T., Borodovsky, M. & Stanke, M. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566 (2021).
Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021).
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
Goel, M., Sun, H., Jiao, W.-B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277 (2019).
Goel, M. & Schneeberger, K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38, 2922–2926 (2022).
Pham, G. M. et al. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience 9, giaa100 (2020).
Nei, M. & Li, W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl Acad. Sci. USA 76, 5269–5273 (1979).
Watterson, G. A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–276 (1975).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Poplin, R. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat. Biotechnol. 36, 983–987 (2018).
Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867–868 (2018).
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19, 153 (2018).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
Reich, D. et al. Reconstructing Indian population history. Nature 461, 489–494 (2009).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Malinsky, M., Matschiner, M. & Svardal, H. Dsuite – fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
Sun, H., Tusso, S. & Schneeberger, K. Haplotype-resolved genome assembly and annotation of tetraploid potatoes (version 2.1). Zenodo https://doi.org/10.5281/zenodo.14053896 (2024).
Weisweiler, M. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. figshare https://doi.org/10.6084/m9.figshare.14604780 (2021).
Sun, H., Tusso, S., Dent, C., Goel, M. & Schneeberger, K. Custom code for analyzing phased pan-genome of tetraploid potatoes. Zenodo https://doi.org/10.5281/zenodo.14786484 (2025).