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Assembly and analysis of repeat-rich regions of plant genomes
 VONDRAK, Tihana
Satellite DNA has been identified in varying proportions in many eukaryotic genomes. It consists of monomeric units arranged in tandem into long, homogeneous arrays. Due to its repetitive nature, satellite DNA is difficult to assemble and analyze, and has therefore been largely neglected in research. With the development of next generation sequencing technologies such as Illumina, research on satellite DNA has intensified and our understanding of it has improved. However, the information we obtain with Illumina reads is limited by their short length. While we can characterize the sequence of satellite DNA and its abundance in genomes, it is not possible to study the long-range organization of satellite DNA, which limits our understanding of the origin and evolution of satellite DNA. This limitation can be addressed by using the latest generation of sequencing technologies that generate much longer reads of tens to hundreds of kilobases. The goal of this work was to develop bioinformatics approaches for analyzing the properties of satellite DNA arrays from long sequence reads or from genome assemblies generated with these reads. These were then used to analyze populations of satellite repeats throughout the genome or in the specific type of chromatin in three plant species that differ in the organization of their centromeres.
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