Onion Genome Sequencing Project

Sequon - Onion Genome Sequencing

To meet the need to produce food for an increasing world population, production levels of food must increase while using less land and inputs such as water, nutrients and pesticides. Onion is an important crop worldwide. For the Netherlands, onion has a high economic value as 90% of the onion bulbs produced in the Netherlands are exported. Dutch breeding companies not only breed onions for the Netherlands and the rest of Europe, but also for the United States, South America, Asia and Australia. In terms of global production value, onion ranks second after tomato. In terms of genetics and genomics, knowledge on the onion genome is scarce compared to tomato. The tomato genome is fully sequenced, whereas little is known about the onion genome. This is partly due to the huge size of the onion genome (16GB). Sequence information is extremely valuable for the identification of genes associated with important traits such as disease resistance and for understanding the underlying mechanisms. The availability of the onion genome will speed up onion breeding and lead to several innovations.


The purpose of this project is to sequence the onion nuclear DNA and provide an ab initio annotated de novo genome assembly.


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 a N50 of 461 Kb. Of this 2.2 Gb was ordered into 8 pseudomolecules using five genetic linkage maps. The remainder of the genome is available in 89.8 K scaffolds. he draft ab initio gene prediction indicated 540 925 putative (pseudo) gene models, of which 86,073 models showed similarity to published proteins (UNIPROT).

Data avilability

The majority of these analysis results will not be archived before publication, but we recognize the need to share them within the Scientific Community. Any individual who accesses information on this site agrees to the Toronto principles will be allowed access to the data. It means that you will:

  • respects the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.
  • will not redistribute, release, or otherwise provide access to the data until the data has been published, submitted to the public data repositories by the Solyntus consortium.
  • will Contact Richard Finkers to discuss any publication plans that utilize this data to avoid the overlap of any planned analyses.
  • will cite accurately and completely the prepublication data, including any applicable version. understands that this data as accessed is precompetitive and is not patentable in its present state.

Resources made available


latest version (140621)

Previous version


This research was supported by a grant from the Top Sector Horticulture & Propagation Materials (H279-SEQUON) and by the companies Bejo Zaden B.V., De Groot en Slot B.V., and GenomeScan. Within the Top Sector, the business community, knowledge institutions and the government work together on innovations in the field of sustainable production of healthy and safe food and the development of a healthy, green living environment.