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

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.

Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single‐cell level

“…Whether these 90 chromosome copies are assembled into 45 assorting units during amitotic division needs to be rigorously tested. We propose to use molecular makers, such as genome‐wide single‐nucleotide polymorphic sites (Chen et al, 2019), rather than phenotypic markers to study assortment kinetics by tracking changes in their frequency during successive amitotic divisions through sequencing (Vitali et al, 2021). This could directly reveal how many assorting units are assembled from the 90 genomic or allelic copies for each MAC chromosome.…”

Regeneration and proliferation of cardiomyocytes and its microRNA regulatory mechanisms

“…Amitosis is recognized as a specialized form of cell division with simple cleavage of the nucleus without the formation of a spindle figure or chromosomes. This process widely exist in prokaryotes and eukaryotes (Vitali et al, 2021), including hepatocytes (David and Uerlings, 1992), pancreatic acinar cells (Nagata, 2003) and macrophages of humans and other mammals (Arkhipov et al, 2008;Il'in et al, 2018;Iljine et al, 2013). So far, little attention has been paid to the role of amitosis in CM proliferation.…”

Photosynthetic Efficiency and Glyco-Metabolism Changes in Artificial Triploid Loquats Contribute to Heterosis Manifestation

“…In the meantime, genome duplication often leads to a larger number of duplicate genes. To maintain the functions well, these duplicate genes undergo a selective loss of some repetitive genes or sequence eliminations [ 13 , 14 ]. For instance, it was found in all studies on Brassica and Tragopogon that the elimination of genome sequences could occur during polyploid formation [ 15 , 16 ], which was precisely because genome duplication could generate the vast majority of duplicate genes and redundant sequences; therefore, understanding the genetic variations after polyploid formation is critical for us to elucidate the process of polyploidization.…”