ArticleNature communications2022
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers, 2 of them syntheses that pooled it.
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Who cites it
104 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- Unlocking the future of crop improvement with crop wild relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Graph-based pangenomics reveals the genetic basis of agronomic traits in tomato fruits.Horticulture research · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Pan-Genomic Dissection of GH1 β-Glucosidases inPlants (Basel, Switzerland) · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean.Nature genetics · 2026Article
- Skeleton-guided 3D digitization standardizes complex trait phenotyping and supports reproducible locus discovery in cucumber.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pan-Genome-Wide Analysis and Expression Profiling of the Potato GST Gene Family.Plants (Basel, Switzerland) · 2026Article
- An updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench].Journal of applied genetics · 2026Article
- Telomere-to-telomere genome assembly and comprehensive mutation library facilitate bitter gourd breeding and functional genomics research.Plant communications · 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
- Graph-based pangenome reveals structural variation dynamics during cucumber breeding.Nature genetics · 2026Article
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.
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