Insights from the first genome assembly of Onion (Allium cepa)

Richard Finkers*, Martijn van Kaauwen, Kai Ament, Karin Burger-Meijer, Raymond Egging, Henk Huits, Linda Kodde, Laurens Kroon, Masayoshi Shigyo, Shusei Sato, Ben Vosman, Wilbert van Workum, Olga Scholten

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

40 Citations (Scopus)


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.

Original languageEnglish
Article numberjkab243
JournalG3: Genes, Genomes, Genetics
Issue number9
Publication statusPublished - 13 Jul 2021


  • DHCU066619
  • Gene space
  • Large genome
  • Repeats
  • ERP111813
  • PRJEB29505


Dive into the research topics of 'Insights from the first genome assembly of Onion (Allium cepa)'. Together they form a unique fingerprint.

Cite this