Homologous Recombination and Transposon Propagation Shape the Population Structure of an Organism fromthe Deep Subsurface with Minimal Metabolism.

DPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus "Forterrea," a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its populationstructure in thedeepsubsurface. Thegenomecontainsmany transposons, yet reconstruction of a complete genome from a short-read insert data set was possible because most occurred only in some individuals. Accuracy of the final reconstruction could be verified because the genome displays the pattern of cumulative GC skew known for some archaea but more typically associated with bacteria. Sequence variation is highly localized, and most pronounced around transposons and relatively close tothe origin of replication. Patternsof variationarebest explainedbyhomologous recombination, aprocess previously not described for DPANN archaea. [ABSTRACT FROM AUTHOR]