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.

Plasticity in Triticeae centromere DNA sequences: a wheat × tall wheatgrass (decaploid) model

“…This analysis identified ~250 k, 211 k, 267 k and 294 k repeat clusters in the tall wheatgrass, CS, XY693 and XY784 genomes, respectively (Figure S5). Then, we mapped the ChIP‐seq and input DNA reads to the repeat clusters and calculated the ratios of ChIP‐seq reads to input reads associated with each cluster (Zhang et al ., ).…”

Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189

“…Therefore, understanding the organization and function of SatDNAs should contribute toward accelerating molecular cytogenetic research in higher plants. Furthermore, SatDNAs can be used to identify homologous chromosomes and determine the positions of centromeres in plants [11,12,14,20,28]. Utilizing the melon genome sequence, we identified new SatDNAs and detected their distributions in melon chromosomes.…”

“…CmSat162 produced major FISH signals on all melon centromeres, and it co-localized with Cmcent, a previously known melon centromere marker (Fig 1). pSat107 and Cmcent shared high sequence homology (Fig 3d), and pSat107 was identified to be Cmcent [20]. CmSat162 and Cmcent were successfully hybridized on metaphase cells of 'Baladewa', 'Ivory F 1 hybrids', and 'P90' (Fig 1d, 1h and 1l).…”

“…Plant centromeres are composed of satellite DNA repeats and highly repeated centromere-specific retrotransposons [15]. Functional centromeres are determined by the occurrence of nucleosomes containing centromere-specific histone H3 (CENH3), the binding of which to DNA can be analyzed by chromatin immunoprecipitation [16,17,18,19,20].…”

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex)

“…Repetitive sequence probes can be combined with FISH to track chromosomal inheritance and analyze karyotypes. To date, C o t-1 DNA, Bacterial Artificial Chromosome (BAC) library, Yeast Artificial Chromosome (YAC) library and chromatin immunoprecipitation (ChIP) methods have been widely applied in combination with FISH to study plant genomes [ 67 – 73 ]. These methods provide tools to obtain chromosome markers that are directly based on their genomic sequences.…”