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Sugarcane ( Saccharum  hybrids  spp .) is the most important sugar crop that accounts for ~75% of the world’s sugar production. Recently, a whole-genome sequencing project was launched on the wild species  S. spontaneum . To obtain information on the DNA composition of the repeat-enriched region of the centromere, we conducted a genome-wide analysis of the DNA sequences associated with CenH3 (a mutant of histone H3 located in eukaryote centromeres) using chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. We demonstrate that the centromeres contain mainly SCEN-like single satellite repeat (Ss1) and several Ty3/ gypsy  retrotransposon-related repeats (Ss166, Ss51, and Ss68). Ss1 dominates in the centromeric regions and spans up to 500 kb. In contrast, the Ty3/ gypsy  retrotransposon-related repeats are either clustered spanning over a short range, or dispersed in the centromere regions. Interestingly, Ss1 exhibits a chromosome-specific enrichment in the wild species  S. spontaneum  and  S. robustum , but not in the domesticated species  S. officinarum  and modern sugarcane cultivars. This finding suggests an autopolyploid genome identity of  S. spontaneum  with a high level of homology among its eight sub-genomes. We also conducted a genome-wide survey of the repetitive DNAs in  S. spontaneum  following a similarity-based sequence clustering strategy. These results provide insight into the composition of sugarcane genome as well as the genome assembly of  S. spontaneum .

Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum