Genomics is the study of the structure, function, evolution, and mapping of genomes. Genomics underwent a major period of transition and progress with the start of the Human Genome Project in 1990. This research spawned several new analysis methods that revolutionized genomics research. This allowed us to question and improve the accuracy of the arbitrary morphological taxonomies used for decades. By identifying appropriate genes, it is easy to build phylogenetic relationships among species. Our research seeks to use a novel computational approach for genome comparison to examine the genus Entamoeba – parasites of humans and other animals. A bioinformatics pipeline is used to align sequences, identify orthologous genes, and calculate the percent similarity between species. Comparsitve genome based on single copy genes showed that there high discrepancies in evolutionary divergences (2-40%) among Entamoeba species. These results demonstrate that classification based on morphology or few genetic markers can undermine the diversity that exists in this group by lumping groups into the same taxonomic ranks. Our findings based on genome scale analysis help in updating the taxonomic classification, so that more accurate information may contribute to conservation biology and the development of targeted medicine used to treat diseases caused by these microorganisms.
