Genomes are often referred to as the “operating system” of living cells and organisms. Analogous to the operating system of a computer or a smart phone, the architecture and the layout of the components within the genome are crucial to the coordination of gene expression and regulation. The genome structures of all living organisms have constantly been under modification over the course of evolution, through both small-scale and large-scale events. By studying the impact of these changes, we have come to understand the functional importance of various genetic elements as well as the regulatory hierarchy among these elements. Recent advances in massively parallel sequencing technology offer power to accurately assemble and reconstruct the genomes from a wide variety of cells and organisms..