Chromosome-level assembly of <i>Cucumis sativus</i> cv. ‘Tokiwa’ as a reference genome of Japanese cucumber

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.