LAUSR

Significance Ciliates are microbial eukaryotes with a unique life cycle: their cells contain two kinds of nuclei, and during development, they eliminate thousands of DNA segments thought to have originated from transposons. Because there are significant differences in DNA elimination between the two best-studied ciliate groups, we sequenced the DNA destined for elimination in Blepharisma, a distantly related species whose phylogenetic position allowed us to evaluate which aspects of the elimination are probably ancestral, including properties of the eliminated DNA and of small RNAs that may target them. We hypothesize that truncated transposon derivatives called MITEs, which are particularly abundant in the eliminated DNA, not only are abundant sources of this DNA but also contribute to retarding its generation.