期刊
GIGASCIENCE
卷 8, 期 6, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giz072
关键词
cucumber; PacBio; Hi-C; genomics; chromosome-scale assembly
资金
- China National Key Research and Development Program for Crop Breeding [2016YFD0100307]
- National Science Fund for Excellent Young Scholars [31322047]
- National Natural Science Foundation of China [31772304]
- National Youth Top-notch Talent Support Program in China
- Science and Technology Innovation Programof Chinese Academy of Agricultural Science (CAAS-ASTIP-IVFCAAS)
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 (similar to 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.
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