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Background Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba). They are model organisms for studies in cellular and evolutionary biology and are of medical and veterinary importance. Despite their importance, Amoebozoan genome organization and genetic diversity remain poorly studied due to a lack of high-quality reference genomes. The slime mold Dictyostelium discoideum is the only Amoebozoan species whose genome is available at the chromosome-level. Results Here, we provide a near-chromosome-level assembly of the Entamoeba histolytica genome, the second semi-completed Amoebozoan genome. The availability of this improved genome allowed us to discover inter-strain heterogeneity in ploidy at the near-chromosome or sub-chromosome level among 11 clinical isolates and the reference strain. Furthermore, we observed ploidy-independent regulation of gene expression, contrary to what is observed in other organisms, where RNA levels are affected by ploidy. Conclusions Our findings offer new insights into Entamoeba chromosome organization, ploidy, transcriptional regulation, and inter-strain variation, which will help to further decipher observed spectrums of virulence, disease symptoms, and drug sensitivity of E. histolytica isolates.

Vesicular trafficking plays an essential role in the expression of virulence competence of the intestinal protozoan parasite E. histolytica that causes amebic dysentery, colitis, and liver abscess in humans, and is responsible for an estimated 50 million cases of amebiasis and 40–100 thousand deaths annually (Haque et al. 2003; Huston 2004). Phagocytosis does not only play a housekeeping role for nutrient uptake, but also participates in various processes essential for colonization and virulence. It has been shown that phagocytosis is involved in the removal of necrotic and apoptotic host cells for colonization and immune evasion (Huston et al. 2003). Indeed, phagocytosis-deficient E. histolytica mutants were defective in the destruction of tissue-cultured mammalian cells in vitro and the formation of hepatic abscesses in vivo (Orozco et al. 1985). In addition to phagocytosis, secretion of digestive proteins including cysteine proteases (CPs) and membrane-permeabilizing peptide amoebapores (APs) has been considered to be responsible for cytopathic activity, i.e., the degradation of host cells and destruction of tissues (Que and Reed 2000; Zhai and Saier 2000). The premise that CPs play a key role in in vitro and in vivo virulence was recently verified by reverse genetic approaches. Overexpression of CP2 caused augmentation of monolayer destruction, but no change in liver abscess formation (Hellberg et al. 2001). In contrast, antisense inhibition of CP5, a putative membrane-bound CP isotype, resulted in a reduced capacity of liver abscess formation (Ankri et al. 1999). These results imply that both secreted and surfacebound CPs are involved in pathogenesis in vitro and in vivo. Interestingly, the above-mentioned phagocytosis-deficient E. histolyticamutants contained a lower level of CPs than the wild-type amebae (Carpeniseanu et al. 2000), suggesting a defect in a pathway shared by phagocytosis and CP secretion, e.g., in trafficking or cytoskeleton, in these mutants. Phagocytosis consists of a number of steps including cell surface binding to ligands and the activation of a signaling pathway leading to F-actin polymerization. In addition, membrane trafficking plays an important role in the controlled maturation of phagosomes. The phagosome maturation is accompanied by sequential fusion with the endocytic and biosynthetic compartments to form a phagolysosome (Stuart and Ezekowitz 2005) and orchestrated by small GTPase, Rab proteins, which act as molecular switches regulating the fusion of vesicles with target membranes through the conformational change between active (GTP-bound) and inactive (GDP-bound) forms (Stenmark and Olkkonen 2001; Takai et al. 2001). Secretion of hydrolytic enzymes is also triggered by a specific ligand– receptor interaction, leading to dynamic vesicular trafficking as well as cytoskeletal reorganization.