MITE infestation of germline accommodated by genome editing in Blepharisma

Abstract

During a sophisticated developmental process, ciliates excise numerous internally eliminated sequences (IESs) from a germline genome copy, producing a functional somatic genome. Most IESs ultimately originate from transposons but homology is obscured by sequence decay. To obtain more representative perspectives on ciliate genome editing, we assembled forty thousand IESs of Blepharisma stoltei, from a much earlier-diverging lineage than existing models. Short IESs (< 115 bp) were largely non-repetitive, with a pronounced ~10 bp length periodicity, whereas longer IESs (max 7 kbp) were non-periodic and contained abundant interspersed repeats. Contrary to current models, the Blepharisma germline genome encodes few transposases. Instead, its most abundant repeat (8000 copies) was a Miniature Inverted-repeat Transposable Element (MITE), apparently a deletion derivative of a germline-limited Pogo-family transposon. We propose MITEs as an important and eventually self-limiting IES source. Rather than defending germline genomes against mobile elements, we argue that transposase domestication actually facilitates junk DNA accumulation.

Origins of genome-editing excisases as illuminated by the somatic genome of the ciliate Blepharisma

“…These sequences are recognized by domesticated transposases whose excision is supported by additional proteins that somehow recognize these marks ( 7 ). Together with MIC sequencing, we observed abundant development-specific sRNA production in Blepharisma resembling other model ciliates ( 36 ). Homologs of proteins implicated in ciliate genome editing were present among the genes most highly differentially up-regulated during new MAC development, notably including Dicer-like and Piwi proteins, which are candidate genes responsible for development-specific sRNA biogenesis and transport ( SI Appendix , Fig.…”

“…There are significant similarities in the basic properties of Blepharisma and Paramecium IESs, detailed in the Blepharisma MIC genome report ( 36 ). Consequently, adopting the Paramecium nomenclature, we refer to the primary candidate IES excisase as Blepharisma PiggyMac (BPgm) and the other somatic homologs as BPgm-Likes (BPgmLs).…”

“…Unlike the conventional transposase-derived genes in B. stoltei , the expression of all these genes throughout the conditions we examined is negligible, and some also appear to be truncated pseudogenes ( Dataset S3 ; workbook “RVT1 + exo_endo_phos_2”). Since it is necessary to understand the relationship of these sequences with respect to IESs, and that they are not due to residual MIC DNA contamination, their analysis is reported in the context of the B. stoltei MIC genome ( 36 ).…”

“…In principle, DNA editing needs to occur in both primary and secondary anlagen to produce functional MAC genomes, since the B . stoltei MIC genome has numerous gene-interrupting IESs ( 36 ).…”

“…In this study, we provide the essential somatic genome and developmental-transcriptomic resources for B. stoltei. As in model ciliates, MIC-limited sequences are removed to form the functional MAC genome ( 36 ). The resulting MAC genome appears to be largely, but not completely, clear of mobile elements and other forms of junk DNA contained in the MIC genome.…”