ArticleGigaScience2020
Construction of a chromosome-scale long-read reference genome assembly for potato.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers.
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Who cites it
190 citing papers in PubMed, 303 citations in OpenAlex.
- Integrated Transcriptomic and Phytohormone Metabolomic Analyses Reveal Distinct Molecular States Associated with PSTVd-Induced Potato Tuber Cracking and Knob-like Protuberances at Tuber Eyes.Plants (Basel, Switzerland) · 2026Article
- Comprehensive Characterization of Cytochrome P450s Reveals Candidate Enzymes Involved in the Metabolic Fate of Absorbed Volatile Organic Compounds in Potato.Antioxidants (Basel, Switzerland) · 2026Article
- Quantitative trait loci for Globodera pallida resistance derived from wild potato species Solanum gourlayi.Journal of applied genetics · 2026Article
- Time-Resolved Developmental and Transcriptomic Profiling of Potato Stolon Initiation from Basal Axillary Buds Following Soil Covering.International journal of molecular sciences · 2026Article
- Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic constraint and hypervariability correlate with fitness effects in elite tetraploid potato breeding material.PLoS genetics · 2026Article
- Comparative Oligo-FISH Mapping Illuminates Chromosomal Evolution Among Rutaceae Species Diverged Over 50 Million Years.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
- Tissue specific mechanisms of tuber dormancy after 1,4-dimethylnaphthalene treatment in potato.Food chemistry. Molecular sciences · 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
- Identification and transcriptome analysis of a major locus for eye depth in tetraploid potato Jinshu 16.BMC plant biology · 2026Article
- Functional potential of the APETALA2 transcription factors StAP2-13/18 in modulating tuberization under long-day (LD) conditions in potato.BMC genomics · 2026Article
- Article
- An AI-powered knowledge hub for potato functional genomics.Plant communications · 2026Article
- Genome-wide characterization of cytochrome P450 genes in Solanum tuberosum and StCYP481 role in salt tolerance.BMC plant biology · 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
- LIKE EARLY STARVATION is involved in the regulation of starch initiation in potato tubers (Solanum tuberosum cv. Désirée).Journal of experimental botany · 2026Article
- Comparative centromere genomics reveals evolutionary divergence in Solanaceae genomes.Genome biology · 2026Article
- Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.G3 (Bethesda, Md.) · 2026Article
- Generating self-incompatible hybrid potatoes through haploid breeding.Nature plants · 2026Article
130 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWorldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost.
findingsHere, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes.
conclusionsAccess to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.