Ciliates are a fascinating model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements. They separate their germline and somatic line into two nuclei within the same cell, and they silence transposons and repetitive elements by way of deleting them from their somatic genome. This large-scale deletion event uses a series of intricate sequence targeting pathways involving small RNAs and transposases, part of which consists of a transnuclear comparison between maternal soma and daughter germline. We present recent progress in this dynamic field, and argue that these DNA targeting pathways provide an optimal system for the transgenerational inheritance of acquired traits. Ciliates thus also demonstrate the evolutionary value of transposable elements, both as sources of sequence diversity and also as drivers of adaptive evolution by necessitating defensive systems.
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