Genomic and Epigenetic Characterization of Sugarcane Hybrids and Wild Relatives

Modern sugarcane cultivars are hybrids of Saccharum officinarum and Saccharum spontaneous species. Hybrids have complex polyploidy genomes that difficult the studies of structure and organization of the genome. Here, we have used high-throughput Illumina sequencing to analyze repeat and genic regions of sugarcane. Genomic DNA was extracted from purified nuclei isolated from leaves of sugarcane SP70-1143 cultivar, and either sheared to 200bp or digested with McrBc. The sugarcane haploid genome size has been estimated at 800Mb; therefore the filtered reads used in this sequence survey represent an estimated 1.58x coverage of sugarcane haploid genome. We compared the Illumina survey sequences with the repeat classifications available from Plant Repeat Database (http://plantrepeats.plantbiology.msu.edu/) to classify each read on the basis of sequence similarity to known repeat sequences. The results provide a snapshot of overall composition of repeat content of sugarcane genome that is not yet sequenced. The McrBC fraction was divided in three samples; the first was sheared to 200 bp, then the 2kb and 5kb fractions were recircularized and sheared to 200 bp. The three fractions were then sequenced and the reads were mapped to the sorghum genome to estimate the coverage of the coding regions. This study is an initial step towards the discovering of structure and organization of sugarcane genome.

Supported by CNPq, FINEP/Genoprot, CAPES and INCT