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

作者：Qing Li, Hongbo Li, Wu Huang, Yuanchao Xu, Qian Zhou, Shenhao Wang, Jue Ruan, Sanwen Huang, Zhonghua Zhang · 发表于：GigaScience · 年份：2019 · DOI：10.1093/gigascience/giz072 · 被引用次数：251 · 研究领域：Advances in Cucurbitaceae Research、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

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...