The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host-parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).

Department of Biochemistry and Molecular Biology Dalhousie University Halifax NS Canada

Department of Biological Sciences University of Alberta Edmonton AB Canada

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

Department of Cell and Molecular Biology Uppsala University Uppsala Sweden

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec Czech Republic

Diversity Ecology and Evolution of Microbes Unité Ecologie Systématique Evolution Université Paris Saclay Orsay France

Division of Infectious Diseases Department of Medicine University of Alberta Edmonton AB Canada

European Molecular Biology Laboratory Genomics Core Facility Heidelberg Germany

Institute of Molecular Genetics Academy of Sciences of the Czech Republic Prague Czech Republic

Institute of Parasitology Biology Centre CAS v v i Ceske Budejovice Czech Republic

School of Biological Sciences University of East Anglia Norwich Research Park Norwich United Kingdom

The Earlham Institute Norwich Research Park Norwich United Kingdom

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