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

Abstract

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.

ArfX2 GTPase Regulates Trafficking From the Trans-Golgi to Lysosomes and Is Necessary for Liver Abscess Formation in the Protozoan Parasite Entamoeba histolytica

“…In our study, the original strain we used was clonal and the genome was sequenced (Kawano-Sugaya et al, 2020), and we obtained virulent and attenuated lines derived from this clonal strain of HM-1:IMSS Cl6 for transcriptomic comparisons. The fact that EhArfX2 was not identified in the two previous studies (Santi-Rocca et al, 2008;Meyer et al, 2016) suggests the presence of multiple mechanisms for attenuation and virulence because no universal gene expression change, either upregulation or downregulation of a gene or a set of genes, was identified in three independent studies (Table 1 and Supplementary Table S2).…”

Trogocytosis in Unicellular Eukaryotes

“…AGCKs are generally activated downstream of class I PI3K [ 136 ]. The E. histolytica genome encodes 24 AGCKs and 6 class I PI3Ks [ 125 , 137 , 138 ]. It is important in future studies to determine whether other AGCKs are also specifically or universally involved in trogocytosis and phagocytosis, and which class I PI3Ks activate such AGCKs.…”

Gene expression of axenically-isolated clinical Entamoeba histolytica strains and its impact on disease severity of amebiasis

“…Moreover, it remains unclear whether observations in laboratory strains are applicable universally, but despite this, studies using clinical strains of E. histolytica are rare because axenic isolation of E. histolytica strains from clinical samples is technically complex and time-consuming. To fill this knowledge gap, we recently launched a project for the collection of clinical strains of E. histolytica, and initiated genomic analysis of these strains [15].…”

“…To fill this knowledge gap, we recently launched a project for the collection of clinical strains of E . histolytica , and initiated genomic analysis of these strains [ 15 ].…”