There are few known cases of archaeal endosymbiosis1,2. Here we present the draft genomes of two such endosymbionts, both living inside eukaryotic ciliates. The hosts in question are Nyctotherus ovalis and Metopus contortus, both known to harbor methane-producing endosymbionts. We have applied culture independent methods such as single cell and metagenomics in order to get insights into the evolutionary history of these organisms. Both methods show remarkably similar results in terms of assembly efficiency and completeness, and both methods seem to be viable methods for whole genome sequencing of endosymbiotic organisms.
Their genomes shows that these are indeed evolutionary separate events, and most likely also recent events. Both endosymbionts show telltale signs of adaptation to endosymbiosis3, albeit at an early stage. Neither of the genomes shows signs of heavy genome size reduction, but there is a gene loss due to pseuodogenization in both genomes, where the endosymbionts of N. ovalis seem to be further along the process. Further study of these genomes might lead to insights into how archaea can escape an eukaryotic hosts defences and adapt to an intracellular lifestyle.