title: Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum.
abstract: 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.
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Wenpan
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Zuo
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Zhanjie
authors.initials: Z
authors.lastname: Li
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Zhuang
authors.initials: Z
authors.lastname: Meng
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Jinlei
authors.initials: J
authors.lastname: Han
authors.affiliation: Texas A&M AgriLife Research Center at Dallas, Dallas, TX 75252, USA.
authors.forename: Junqi
authors.initials: J
authors.lastname: Song
authors.affiliation: USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA.
authors.forename: Yong-Bao
authors.initials: YB
authors.lastname: Pan
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|Key Laboratory of Education Ministry for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.|National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D002503:Centromere / Q000235:genetics*; D004251:DNA Transposable Elements; D018745:Genome, Plant; D006657:Histones / Q000235:genetics; D011003:Ploidies; D012091:Repetitive Sequences, Nucleic Acid; D031786:Saccharum / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D006657:Histones