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

View ORCID ProfileRichard 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
doi: https://doi.org/10.1101/2021.03.05.434149
Richard Finkers
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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  • ORCID record for Richard Finkers
  • For correspondence: richard.finkers@wur.nl
Martijn van Kaauwen
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Kai Ament
2Bejo Zaden B.V., Trambaan 1, 1749 CZ Warmerhuizen, The Netherlands
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Karin Burger-Meijer
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Raymond Egging
3GenomeScan, Plesmanlaan 1d, 2333 BZ Leiden, The Netherlands
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Henk Huits
2Bejo Zaden B.V., Trambaan 1, 1749 CZ Warmerhuizen, The Netherlands
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Linda Kodde
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Laurens Kroon
2Bejo Zaden B.V., Trambaan 1, 1749 CZ Warmerhuizen, The Netherlands
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Masayoshi Shigyo
4Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University Yamaguchi City, Yamaguchi 753-8515, Japan
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Shusei Sato
5Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
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Ben Vosman
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Wilbert van Workum
6Limes Innovations B.V., Ruigekade 1, 2351 SX Leiderdorp, The Netherlands
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Olga Scholten
1Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Abstract

Onion is an important vegetable crop with an estimated genome size of 16Gb. 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 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. 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, 86,073 showed similarity to published proteins (UNIPROT). No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with A. 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 05, 2021.
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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
bioRxiv 2021.03.05.434149; doi: https://doi.org/10.1101/2021.03.05.434149
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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
bioRxiv 2021.03.05.434149; doi: https://doi.org/10.1101/2021.03.05.434149

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