An overview of genetic manipulation tools in the studies of ciliates, with emphasis on gene knockout, knockdown, and overexpression

Abstract Microorganisms have expanded our understanding of biodiversity and exhibit crucial research values. Ciliated protists are a highly differentiated group of eukaryotic microorganisms with exceptional features, such as numerous cilia, dimorphic nuclei, and genome-wide gene rearrangement, that have made them ideal research models for revealing many biological processes. Studies of the ciliate Tetrahymena thermophila have greatly advanced our understanding of RNA self-splicing and enzymatic activity, telomere biology, and the Nobel Prize-winning telomerase mechanisms. Genome rearrangement during the sexual reproduction (conjugation) of ciliates, involving the elimination of ~25–90% of germline DNA, provides an opportunity to study large-scale genome remodelling while also revealing a more thorough mode of transposon repression, i.e. Piwi-interacting small RNA-mediated DNA deletion in the somatic nucleus. Although much progress has been made, research has focused mainly on a few model species that are amenable to gene editing. For other species, although they are more suitable to address some scientific gaps, research cannot be carried out owing to limitations of genetic engineering. Here, we summarize the existing genetic engineering strategies for ciliates, expecting to provide inspiration for the development and optimization of genetic engineering tools for ciliates and other organisms cannot yet be edited genetically.