Organization and Complexity of the Repeat-Rich Fraction of the Sugarcane Genome

Modern sugarcane cultivars are hybrids of Saccharum officinarum and Saccharum spontaneum species. Hybrids have complex polyploidy genomes that difficult the studies of structure and organization of the genome. To understand the structure of the repeat rich fraction of the sugarcane genome, total DNA from the wild parents Saccharum officinarum and Saccharum spontaneum, and three commercial cultivars – B4362, RB867515 and RB72454 - was sheared to 200bp and sequenced by Illumina. To study the organization and complexity of the repeat rich fractions of each sample, we compared the 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. Comparison of the main repeat fractions has shown significant differences in the abundance of the families of repeats among the genotypes, but also has shown that qualitative differences in repeat presence in the wild parents and commercial cultivars.This study is an initial step towards the discovering of structure and organization of sugarcane genome.

Supported by FAPERJ, CAPES, INCT/CNPq