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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #335843
Title: Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum

Author
item ZHANG, WENPAN - Fujian Agriculture And Forest University
item ZUO, SHENG - Fujian Agriculture And Forest University
item LI, ZHANJIE - Fujian Agriculture And Forest University
item MENG, ZHUANG - Fujian Agriculture And Forest University
item HAN, JINLEI - Fujian Agriculture And Forest University
item SONG, JUNGI - Texas Agrilife Research
item Pan, Yong-Bao
item WANG, KAI - Fujian Agriculture And Forest University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2016
Publication Date: 1/30/2017
Publication URL: http://handle.nal.usda.gov/10113/5661730
Citation: Zhang, W., Zuo, S., Li, Z., Meng, Z., Han, J., Song, J., Pan, Y.-B., Wang, K. 2017. Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum. Scientific Reports. 7:41659. doi:10.1038/srep41659(2017).

Interpretive Summary: Sugarcane is the most important sugar crop in the world that accounts for about 75% of total sugar production. Characterization of sugarcane’s genetic makeup by DNA sequencing, however, is far behind other crops because sugarcane is an inter-specific hybrid between at least two wild progenitor species. Recently, a DNA sequencing project was launched on one of the progenitor species, Saccharum spontaneum, targeting its entire genetic material or whole genome in other words. This study was designed to assist in the project by investigating the composition of DNA sequence repeat-enriched regions along centromere, a key structure on chromosomes to guide orderly chromosome separation during cell division. Two molecular tools, namely, ChIP (chromatin immunoprecipitation) with CenH3 marker and FISH (fluorescence in-situ hybridization), were used to characterize the DNA composition of the centromeres of all chromosomes in the cells of leaf tissue and visualize where the CenH3 markers hybridize to the chromosomes in the root tip cells. The results showed that CenH3-like markers Ss1 and Ty3/gypsy were either clustered or dispersed in the centromeres. Ss1 marker exhibited a chromosome-specific enrichment in the wild progenitor species S. spontaneum and S. robustum, but not in domestic sugarcane. The results also indicated that there were eight duplicated sets of eight chromosomes in the S. spontaneum clone SES208 and Ss1 marker was highly conserved among the eight homologous chromosomes. These results provide new knowledge to sugarcane genetics by facilitating the assembly of DNA sequences into a complete genome of SES208.

Technical 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.