The genome is a common feature of all cellular organisms and contains a comprehensive record of evolution. At a closer look, the genome is in fact a ‘genomic microcosm’ – a smörgåsbord of interactions among/between host genes and parasitic genes, such as transposons and viruses. We study how these genomic parasites impact genome structure and speciation of birds, crocodilians, arthropods, and parasitic nematodes. Beware, some of these jumping genes even jump between genomes! Our group is currently adding two new main focal areas that synthesize our exciting findings on this topic over the last 6 years: We have recently shown that two thirds of all 10,500 bird species have extensive germline/soma genome differences (Ruiz-Ruano, ..., Suh, in prep.), how these genome differences arise during development using spatial and bulk transcriptomics (Vontzou, ..., Suh, in prep.) and that centromere repositioning may be frequent in birds and lead to similar evolutionary outcomes in the absence of inversions, but requires ultra-long reads to assemble and place Megabase-scale centromeric satellite repeat arrays (Westerberg, ... Suh, in prep; Borges, ... Suh, in prep.). We are in the process of generating even larger amounts of genome data from germline and soma samples of various animals as we strive towards telomere-to-telomere genome assemblies, complete gene/repeat annotations, and large whole-genome alignments of hundreds of non-model organisms.