Genome content reorganization in the non-model ciliate <i>Chilodonella uncinata</i> : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development

Ciliates are a clade of diverse single-celled eukaryotic microorganisms that contain at least one somatic macronucleus (MAC) and germline micronucleus (MIC) within each cell/organism. Ciliates rely on complex genome rearrangements to generate somatic genomes from a zygotic nucleus. However, the development of somatic nuclei has only been documented for a few model ciliate genera, including <i>Paramecium</i>, <i>Tetrahymena</i>, and <i>Oxytricha</i>. Here, we study the MAC developmental process in the non-model ciliate, <i>C. uncinata</i>. We analyze both total DNA and the generation of gene-sized somatic chromosomes using a laser scanning confocal microscope to describe <i>C. uncinata</i>'s nuclear life cycle. We show that DNA content changes dramatically during their life cycle and in a manner that differs from previous studies on model ciliates. Our study expands knowledge of genome dynamics in ciliates and among eukaryotes more broadly.