ArticleGenome biology2023
A super-pangenome of the North American wild grape species.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Integrated pangenomics and population genomics reveal climate adaptation and maladaptation in an East Asian tree.Nature communications · 2026Article
- Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- The dynamics of introgression and parallel adaptation across North AmericanProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's disease in Vitis arizonica and its hybrids.G3 (Bethesda, Md.) · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Genetic Diversity and Core Germplasm Development in Yunnan Tartary Buckwheat Based on Phenotypic and SNP Data.Plants (Basel, Switzerland) · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Hybrid Whole-Genome Sequencing for Genetic Stability Assessment of Infectious Laryngotracheitis Virus Vaccine Strains.Vaccines · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- Haplotype-resolved T2T gap-free genomes of the winegrape cultivar Cabernet Sauvignon.Scientific data · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Genetic and physiological mechanisms of grapevine resistance toFrontiers in plant science · 2026Review
- Evolutionary analysis of ascorbate-glutathione cycle genes across green plants with lineage-specific profiling in grapevine (Horticulture research · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
2 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
backgroundCapturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.
resultsHere we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.
conclusionsThis study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
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