PT - JOURNAL ARTICLE AU - Alexander J Probst AU - Jillian F. Banfield TI - Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism AID - 10.1101/249516 DP - 2018 Jan 01 TA - bioRxiv PG - 249516 4099 - http://biorxiv.org/content/early/2018/01/17/249516.short 4100 - http://biorxiv.org/content/early/2018/01/17/249516.full AB - 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 population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert dataset 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 to the origin of replication. Patterns of variation are best explained by homologous recombination, a process previously not described for DPANN archaea.