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Abstract

Each ciliate cell has two types of nuclei: the germline micronucleus (MIC), which is usually transcriptionally silent, and somatic macronucleus (MAC), where most gene expression takes place. In most ciliates, MACs develop from MIC precursors following sexual conjugation. Thousands of interspersed DNA segments called internally eliminated sequences (IESs) ranging from 10s to 1000s bp length are eliminated, and chromosomes also experience fragmentation, rearrangement, and amplification, although the extent varies between species. The MAC genome content is hence a subset of the MIC genome. Here we report an apparent lack of IESs in the ciliate Loxodes magnus. We separated MIC and MAC by flow cytometry and confirmed purity by morphology and Western blotting against MAC-specific markers. Unexpectedly, sequence libraries prepared from purified nuclei showed only a small fraction of k-mers specific to the MIC libraries. Indels found by mapping MIC reads against MAC draft genomes appeared to represent allele variants rather than IESs. Both genomes were relatively large: after filtering out low-complexity repetitive sequences (up to 43% of total), assemblies were 450-470 Mbp (MAC) vs. 460-480 Mbp (MIC). There may hence be some MIC-limited genome content, but not in the form of typical abundant interspersed IESs. Nonetheless, histone markers and nucleosome profiling suggest that the MACs are the site of active gene expression, like other ciliates. Loxodes belongs to the class Karyorelictea, whose MACs cannot divide vegetatively unlike other ciliates, and so are obliged to undergo MIC-MAC development for every cell division, including vegetative divisions. We hypothesize that the loss or streamlining of genome editing may be a way to avoid costly overheads during cell division.