Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

Valerio Vitali,Francesco Catania,Rebecca Rothering

doi:10.3390/microorganisms9091979

Valerio Vitali, Francesco Catania + Show 1 more

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https://doi.org/10.3390/microorganisms9091979

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Journal: Microorganisms	Publication Date: Sep 17, 2021
Citations: 4	License type: CC BY 4.0

Affiliation: University of Münster

Abstract

Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis.

Highlights

The commonly held view that mitosis and meiosis are the universal forms of cell division is incomplete—some cells can divide without the intervention of the nuclear spindle following direct nuclear fission, a process known as amitosis
We first assessed the quality of the scDNA-seq data in terms of somatic genome representation, focusing on two common sources of coverage bias associated with multiple displacement amplification (MDA), namely genome composition (GC content) and position along the chromosomes
McDNA-seq and aDNA-seq show negligible GC Bias—i.e., a virtually homogeneous coverage across the whole range of GC-content found in Paramecium genome

Summary

Introduction

The commonly held view that mitosis and meiosis are the universal forms of cell division is incomplete—some cells can divide without the intervention of the nuclear spindle following direct nuclear fission, a process known as amitosis. Many of its early accounts (e.g., [1]) have been disproved [2], its occurrence considered a rare exception [3], an aberrant or degenerative process [4], or a form of nuclear division strictly uncoupled from cell proliferation [5]. In ciliates, amitosis has evolved into the predominant means of somatic nuclear reproduction during cell proliferation [11]. In Drosophila, amitosis of polyploid cells in the intestinal epithelium may serve as a significant mechanism of de-differentiation associated with stem cell replenishment [7]

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