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

Tetsuro Kawano-Sugaya,Yasuaki Yanagawa,Shinji Izumiyama,Tomoyoshi Nozaki,Seiki Kobayashi,Kumiko Nakada-Tsukui,Koji Watanabe,Yumiko Saito-Nakano

doi:10.1186/s12864-020-07167-9

Abstract

BackgroundAmoebozoa 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.ResultsHere, 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.ConclusionsOur 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.

Highlights

Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba)
After construction of several assemblies using HGAP3 [8], HGAP4, and Flye [9], HGAP3 was the most redundant and lossless assembly, representing 35 Mb fragmented into 403 contigs that were scaffolded with Hi-C reads
The near-chromosome level scaffolds were arranged by JuiceBox [10], and gaps were filled using PBjelly [11]

Summary

Introduction

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. Entamoeba histolytica is an intestinal protozoan parasite that causes human amebiasis. It is a major causative agent of diarrheal diseases, which was ranked fifth in the 2015 list of diseases responsible for high disabilityadjusted life years (DALYs) [1]. Due to its medical importance and biological peculiarities, the first draft genome of the E. histolytica HM-1: IMSS reference strain was reported in 2005 [4]. The genome structure predicted by the first draft was highly fragmented, due to the repetitive nature of the genome (e.g. short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), tRNA arrays containing short tandem repeats [6], segmental duplications, and polyploidy), which complicates chromosome-level genome characterization

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