Seiko Takashi, Muto Chiaki, Shimomura Koichiro, Yano Ryoichi, Kawazu Yoichi, Sugiyama Mitsuhiro, Kato Kenji, Tomooka Norihiko, Naito Ken
Research Center of Genetic Resources, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
Breed Sci. 2025 Apr;75(2):85-92. doi: 10.1270/jsbbs.24066. Epub 2025 Mar 27.
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.
黄瓜是日本市场上最重要的蔬菜之一。为了促进基于基因组学的育种，对日本黄瓜的参考基因组有需求。然而，尽管黄瓜基因组相对较小，但由于串联重复序列占基因组的约30%（约100兆碱基对），其组装是一个具有挑战性的问题。为了克服这一问题，我们采用了牛津纳米孔测序技术，该技术可产生N50长度大于30千碱基对的长读长。利用这项技术，我们实现了对‘常盘’品种的染色体水平组装，‘常盘’是日本黄瓜的一个创始品系，以细长的果实形状和高脆质地为特征。与现有的黄瓜基因组相比，‘常盘’基因组长20%，注释的基因多10%。利用纳米孔长读长进行的组装还解析了跨度超过100千碱基对的串联重复序列，证明了其在克服重复序列方面的优势。
