The availability of complete genome sequences for many eukaryotic organisms continues to contribute towards a better understanding of their genome design and evolution. This investigation involves computational analysis of genome architecture of 6 eukaryotic genomes (4 vertebrate: H.sapiens, P.troglodytes, M.musculus, D.rerio; 2 invertebrate: C.elegans, D.melanogaster). We further analyzed the drug targets, that is, proteins in the human genome with FDA (Food and Drug Administration) approved drugs using various parameters such as protein interacting partners, number of exons, number of pathways, number of tissues and protein family to find if there is any co-relation between these parameters and the targetability of the protein. It was observed that proteins from single exonic genes are more likely to have an FDA approved drug. These data have implications in understanding eukaryotic genome design and may also contribute in drug target selection which is the most important step in drug discovery. Further, a database was constructed on discordant introns. These investigations will help us in understanding eukaryotic genome design.