ArticleG3 (Bethesda, Md.)2021
Insights from the first genome assembly of Onion (Allium cepa).
Article in G3 (Bethesda, Md.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of theInternational journal of molecular sciences · 2026Article
- Using reciprocally retained gene families to detect whole-genome multiplications in plants.Genome biology · 2026Article
- Identification and analysis of small RNAs in exosome-like nanoparticles derived from onion (Biochemistry and biophysics reports · 2026Article
- Recent progress in DNA marker-assisted selection for vegetable breeding in Japan.Breeding science · 2026Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- Identification of a gene coding for a pentatricopeptide repeat protein as a candidate responsible for theMolecular breeding : new strategies in plant improvement · 2025Article
- Identification and analysis of the GATA gene family in onion (Allium cepa L.) in response to chromium and salt stress.BMC genomics · 2025Article
- Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.).Scientific data · 2025Article
- Host-resistance inFrontiers in plant science · 2025Article
- Navigating Amaryllidaceae alkaloids: bridging gaps and charting biosynthetic territories.Journal of experimental botany · 2025Review
- Metabolomics revealed the characteristics of the unique flavor substances of AlxaFood chemistry: X · 2024Article
- Review
- Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- AlliumDB: a central portal for comparative and functional genomics inHorticulture research · 2024Article
- A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences.BMC genomics · 2024Article
- Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion.3 Biotech · 2024Article
- Chromosome-level genomes of three key Allium crops and their trait evolution.Nature genetics · 2023Article
- Development of SNP markers linked to purple blotch resistance for marker-assisted selection in onion (3 Biotech · 2023Article
- The Control of the Crossover Localization in Allium.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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