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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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-020-07167-9.

Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica