Bioinformatics Approach to Identify Physical Locations of Telomeric, Centromeric and Nucleolus Organizing Regions in Cultivated Sunflower

Centromeres and telomeres are essential genetic structures found at the arms and tips of chromosomes, respectively, while nucleolus organizing regions are chromosomal areas that contain multiple copies of ribosomal RNA genes. These regions ensure proper segregation and function of chromosomes and are comprised of high-copy tandem repeats. Although the function of centromeres is highly conserved as the site of assembly of the kinetochore, phylogenetic analysis of centromeric sequence shows little sequence conservation. In contrast, telomeric tandem repeats of 5'-TTTAGGG-3' are well conserved in plants. By using whole genome shotgun (WGS) sequence data from Roche 454 and Illumina sequencing platforms, we developed a bioinformatics pipeline to identify telomeric, centromeric and nucleolus organizing regions in cultivated sunflower, Helianthus annuus. We used mate-paired libraries to anchor these repeats to mapped portions of the genome. Results suggest that this method can be used to computationally place most of the telomeric, centromeric, and nucleolus organizer regions in repetitive genomes.