ArticleBreeding science2025
Chromosome-level assembly of
Article in Breeding science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Recent progress in DNA marker-assisted selection for vegetable breeding in Japan.Breeding science · 2026Article
- 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.Molecular ecology · 2025Article
- Current and future pangenomic research in cucurbit crops.Breeding science · 2025Article
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Authors and funding
9 authors.
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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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