Mention 2 characteristics that can be used to distinguish a eukaryotic genome from a prokaryotic genome Solution The two major difference between genome of eukaryotic and prokaryotic genomeare: 1. Prokaryotic genome contains only one chromosome and eukaryotic genome contains multiple chromosomes. prokaryotic genome is found in cytoplasm while eukaryotic genome is found in nucleus. 2. Generally prokaryotic DNA is circular in structure known as plasmid with few exceptions. Eukaryotic DNA is linear. The eukaryotic genome is more complex with longer genes..