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.
Show 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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