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

Massive DNA excision occurs regularly in ciliates, ubiquitous microbial eukaryotes with somatic and germline nuclei in the same cell. Tens of thousands of internally eliminated sequences (IESs) scattered throughout the ciliate germline genome are deleted during the development of the streamlined somatic genome. The genus Blepharisma represents one of the two high-level ciliate clades (subphylum Postciliodesmatophora) and, unusually, has dual pathways of somatic nuclear and genome development. This makes it ideal for investigating the functioning and evolution of these processes. Here we report the somatic genome assembly of Blepharisma stoltei strain ATCC 30299 (41 Mbp), arranged as numerous telomere-capped minichromosomal isoforms. This genome encodes eight PiggyBac transposase homologs no longer harbored by transposons. All appear subject to purifying selection, but just one, the putative IES excisase, has a complete catalytic triad. We hypothesize that PiggyBac homologs were ancestral excisases that enabled the evolution of extensive natural genome editing.

Automated summary

Ciliates are microbial eukaryotes that undergo massive DNA excision during the development of their somatic genome. In this study, the somatic genome assembly of Blepharisma stoltei was reported, revealing the presence of PiggyBac transposase homologs that were no longer associated with transposons. These homologs are subject to purifying selection, with one being a putative IES excisase with a complete catalytic triad. It is hypothesized that PiggyBac homologs were ancestral excisases that enabled extensive natural genome editing.