Genome-Wide Characterization of Cucumis hystrix Repetitive Sequences Derived from Next-Generation Sequence Reads

Cucumis hystrix Chakr. (2n=2x=24), bearing multiple disease-resistance, is the only wild species cross-compatible with cucumber in Cucumis genus. Repetitive DNAs, including transposable elements and tandem repeats, are the major components in eukaryotic genomes as well as the important factors contributing to chromosome evolution. Although a draft assembly of C. hystrix genome was available in 2014 and some repetitive DNAs studies have been reported, the characterization of repetitive elements has not been a subject of detailed analysis. In this study, genome-wide characterization using graph-based clustering analysis showed that about 19% of the genome was composed of repetitive sequences. Four kinds of differentially amplified tandem repeats, including Cucumis hystrix satellite 1-3 (CuhySat1-CuhySat3) and Cuhy5S, were identified and characterized in detail using bioinformatics and fluorescence in situ hybridization (FISH). The CuhySat satellites localized at the subtelomeric regions of all chromosomes, it is consistent with genomic in situ hybridization (GISH) result, and Cuhy5S produced one pair of interstitial signals. These results provide a more comprehensive acknowledgement of C. hystrix genome repetitive composition and would be helpful for illustrating chromosome evolution in Cucumis.