A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). Issue 6 (18th June 2019)

• Record Type: Journal Article
• Authors: Li, Qing; Li, Hongbo; Huang, Wu; Xu, Yuanchao; Zhou, Qian; Wang, Shenhao; Ruan, Jue; Huang, Sanwen; Zhang, Zhonghua
• Is Part Of: GigaScience. Volume 8:Issue 6(2019)
• Publication Date: 2019-06-18
• Subjects: cucumber -- PacBio -- Hi-C -- genomics -- chromosome-scale assembly; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giz072
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: 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. Findings: 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. Conclusion: 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.