Despite differing in several fundamental features of eukaryotic nuclei, the MAC is derived from a mitotic sibling of the MIC during sexual reproduction in a process that involves extensive, genome-wide programmed DNA rearrangements. Although unicellular, ciliates carry two distinct nuclei that display a remarkable form of germline/soma differentiation ( Figure 1A Orias et al., 2011) the smaller, diploid, transcriptionally silent germline nucleus (micronucleus or MIC) contains the genetic material transmitted across sexual generations, whereas the larger, polyploid, actively expressed somatic nucleus (macronucleus or MAC) supports all the vegetative functions of the cell. This large-scale phenomenon has been most thoroughly studied in the phylum Ciliophora, or ciliates, a deep-branching and diverse group of protozoa ( Bracht et al., 2013 Chalker and Yao, 2011 Coyne et al., 2012 Vogt et al., 2013 Yao et al., 2014). Other cases result in genome-wide chromosome restructuring, as was first recognized by microscopic observation of parasitic nematodes over 125 years ago ( Boveri, 1887) and since documented in several eukaryotic branches, including vertebrates ( Bachmann-Waldmann et al., 2004 Smith et al., 2012 Sun et al., 2014 Wang and Davis, 2014). Some cases mediate the generation of protein products specific to a differentiated cell type, such as sigmaK of the Bacillus subtilis mother cell ( Kunkel et al., 1990) or the vast diversity of vertebrate immunoglobulins ( Schatz, 2004). The establishment of distinct genomic lineages (cellular or nuclear) in the life cycles of phylogenetically diverse organisms has allowed the evolution of a wide variety of programmed, somatic lineage-specific DNA rearrangement mechanisms. We also compare Tetrahymena’s germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. MRC Laboratory of Molecular Biology, United Kingdom.The Johns Hopkins University School of Medicine, United States.Institute of Molecular Biotechnology, Austria.Broad Institute of Harvard and MIT, United States Southern Illinois University, United States.University of Utah School of Medicine, United States.University of California, Santa Barbara, United States.
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