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bioRxiv · 10.1101/2024.04.15.589484

Chromosome-level assembly of Cucumis sativus cv. 'Tokiwa' as a reference genome of Japanese cucumber

Seiko, T.·Muto, C.·Shimomura, K.·Yano, R.·Kawazu, Y.·Sugiyama, M.·Kato, K.·Tomooka, N.·Naito, K.
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Abstract

Cucumber is one of the most important vegetables in the Japanese market. To facilitate genomics-based breeding, there is a demand for reference genome of Japanese cucumber. However, although cucumber genome is relatively small, its assembly is a challenging issue because of tandem repeats comprising [~]30% ([~]100 Mbp) of the genome. To overcome, we deployed the Oxford nanopore sequencing that produces long reads with N50 length of >30 kbp. With this technology we achieved a chromosome-level assembly of cv Tokiwa, a founder line of Japanese cucumber represented with the elongated fruit shape and high-crisp texture. Compared to the existing cucumber genomes, the Tokiwa genome is 20% longer and annotated with 10% more genes. The assembly with nanopore long reads also resolved tandem repeats spanning >100 kbp, demonstrating its strength in overcoming repetitive sequences.

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Seiko, T., Muto, C., Shimomura, K., Yano, R., Kawazu, Y., Sugiyama, M., Kato, K., Tomooka, N., Naito, K.. 2024-04-17. Chromosome-level assembly of Cucumis sativus cv. 'Tokiwa' as a reference genome of Japanese cucumber. https://doi.org/10.1101/2024.04.15.589484

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