Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entam
- PDF / 2,270,218 Bytes
- 8 Pages / 595.276 x 790.866 pts Page_size
- 79 Downloads / 153 Views
RESEARCH ARTICLE
Open Access
Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica Tetsuro Kawano-Sugaya1,2†, Shinji Izumiyama2†, Yasuaki Yanagawa3, Yumiko Saito-Nakano2, Koji Watanabe3, Seiki Kobayashi4, Kumiko Nakada-Tsukui1,2 and Tomoyoshi Nozaki1*
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. Keywords: Entamoeba, Aneuploidy, Expression regulation, Hi-C, PacBio
Background 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]. E. histolytica resides in the large intestine, which represents an anaerobic * Correspondence: [email protected] † Tetsuro Kawano-Sugaya and Shinji Izumiyama contributed equally to this work. 1 Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan Full list of author information is available at the end of the article
environment. Thus, it has evolved unique core metabolism, mitochondrial structure and function, and cellular activities, such as compartmentalized sulfate activation in the mitochondrion-related organelle (mitosome) [2] and internalization of live mammalian cells by trogocytosis [3]. 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 first reported assembly was 23.8 Mb long with 12.5-fold coverage and was segmented into 888 scaffolds. In the
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits u
Data Loading...
