Chromosome-Scale Genome Assemblies of Two Korean Cucumber Inbred Lines

Practicing traditional food habits and using traditional ingredients are of major importance for maintaining a diet with good nutritional value. South Korea is well known for its fermented foods, particularly banchan (fermented side dishes such as kimchi), which are deeply rooted in Korean food culture. Moreover, Korean cuisine has unique characteristics that are widely accepted to provide various health benefits (Kim et al., 2016), with Korean food culture involving high consumption of vegetables due to the characteristics of its long agricultural history. According to the KoreanMinistry of Agriculture definition of the standards and fundamentals of Korean food, one major constraint is that only food prepared with ingredients produced or cultivated in Korea can be considered Korean food. For example, kimchi prepared from imported Chinese cabbage cannot be considered Korean food; the same applies to other banchan. As part of the process of preserving Korean food culture, we have initiated the development of genetic resources for Korean varieties of cucumber (Cucumis sativus var. sativus L.), which is widely cultivated in Korea for both fresh and processed consumption. Cucumber originated in India and spread to other parts of the world through adaptation to various environmental factors and indigenous food habits (Sebastian et al., 2010). This process has led it to become the sixth most widely cultivated vegetable crop in the world, with 2.1 million hectares under cultivation (FAOSTAT, 2020). South Korea is the 16th largest producer of cucumber in the world, with three major cultivar groups being grown: the Baekdadagi-type, Nakhap-type, and Gasi-type cultivars (Park et al., 2021). In this study, we aimed to obtain detailed insights into the genetics of cucumber varieties by constructing chromosome-scale genome assemblies for two Korean cucumber inbred lines: JEF (semi-white Baekdadagi-type, mainly used for kimchi and other fermented foods) and KWS (Korean solid green, Nakhap-type, a slicer used fresh for salads and gimbap or Korean cold noodles). As shown by previous studies of model plants and crops, a single reference genome is inadequate to capture the variation among different genetic lineages. For example, significant structural variation among maize inbred lines has been identified through analysis of multiple genomes (Tao et al., 2019). Furthermore, the cost of assembling multiple genomes has been significantly reduced by third-generation sequencing technologies and computational methods, leading to the construction of chromosome-scale genome assemblies for various crops with the aim of obtaining detailed insights into gene–trait associations (Yang et al., 2019). The first version of the cucumber draft genome was released in 2009 for inbred line 9,930, a lineage of the ‘Chinese Long’ cultivar (Huang et al., 2009); the genome has since been updated to version 3 (Li et al., 2019) and the chromosomal level Northern American cucumber genome published in 2012 (Yang et al., 2012). Further insight into variations among and within varieties has recently been provided by the Edited by: Yiqun Weng, University of Wisconsin-Madison, United States