ArticleNature genetics2023
Chromosome-level genomes of three key Allium crops and their trait evolution.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 31 papers.
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31 citing papers in PubMed, 48 citations in OpenAlex.
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- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- The Nigella damascena genome provides insights into transposable element-driven genomic gigantism and trait evolution.Nature communications · 2026Article
- Laminar patterning transcription factors orchestrate spatial metabolite partitioning in Capsicum fruit.Nature plants · 2026Article
- Article
- A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of theInternational journal of molecular sciences · 2026Article
- Domestication and genome evolution iniScience · 2026Review
- Using reciprocally retained gene families to detect whole-genome multiplications in plants.Genome biology · 2026Article
- Molecular mechanisms of root expansion in medicinal plants.Frontiers in plant science · 2026Review
- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- Omics landscapes in molecular mechanisms withFood chemistry. Molecular sciences · 2025Review
- A closed-loop method for precise genome size estimation using HiFi reads.BMC genomics · 2025Article
- Establishment of Transient Transformation Systems in Welsh Onion (Plants (Basel, Switzerland) · 2025Article
- Pancentromere analysis of Allium species reveals diverse centromere positions in onion and gigantic centromeres in garlic.The Plant cell · 2025Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- Identification of S-1-propenyl-Food chemistry. Molecular sciences · 2025Article
- A premature termination codon mutation in the onionHorticulture research · 2025Article
- Identification of a gene coding for a pentatricopeptide repeat protein as a candidate responsible for theMolecular breeding : new strategies in plant improvement · 2025Article
- A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic.Horticulture research · 2025Article
- Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.).Scientific data · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
33 authors at 9 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.
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