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Gigascience. 2019 Jun 1;8(6). pii: giz072. doi: 10.1093/gigascience/giz072.

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).

Author information

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China.
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen 518124, China.
College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China.



Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential.


We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (∼211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants.


This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.


Hi-C; PacBio; chromosome-scale assembly; cucumber; genomics

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