Development of an algorithm for the assembly of the sugarcane polyploid genome

Abstract

The challenges in sequencing the sugarcane genome relies in the assembly and to analyze a highly complex genome that is polyploid and aneuploid, with a complete set of homologous genes predicted to range from 10 to 12 copies (alleles). The present project aim to improve, through the development of new algorithms, the assembly from shotgun reads of datasets generated by the BIOEN research groups. We intend to combine shot-gun sequencing data obtained using 454 and Illumina using different protocols to assemble a reference genome for cultivar SP80-3280. To accomplish assembly the group will develop algorithms to enable the recognition of multiple copies of any given region of the reference genome. The group will perform comparative analysis with other genomes, especially sorghum that is very synthenic to sugarcane, to evaluate the quality of the assembled sequence. Existing data on the sugarcane transcriptome will be integrated to validate gene models and infer gene function. Microsoft will develop algorithms for assembly of the sugarcane polyploid genome to strengthen allele Identification and improve assembly. The results will contribute to the advancement of knowledge in plant genomics, establishment of computational infrastructure and the formation of highly qualified human resources in bioinformatics. In the long term, we expect to create computational biology tools to resolve polyploid genomes first with the sugarcane genomics but that may also be applied to other cultivated polyploid crops. (AU)