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

Abstract 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 analys...

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Published inGenome biology and evolution Vol. 10; no. 4; pp. 1115 - 1119
Main Authors Probst, Alexander J, Banfield, Jillian F
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.04.2018
Society for Molecular Biology and Evolution
Subjects
archaea
Archaea - genetics
Archaea - metabolism
Bacteria - genetics
Bacteria - metabolism
BASIC BIOLOGICAL SCIENCES
complete genome
DNA Transposable Elements - genetics
DPANN
Genetics, Population
Genome Report
Genome, Archaeal - genetics
homologous recombination
Homologous Recombination - genetics
Metagenomics
transposon
transposon
homologous recombination
complete genome
metagenomics
DPANN
archaea
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Summary:Abstract 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 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 to the origin of replication. Patterns of variation are best explained by homologous recombination, a process previously not described for DPANN archaea.
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AC02-05CH11231
USDOE Office of Science (SC)
Data deposition: This project has been deposited at NCBI under the BioProject number PRJNA405984. The genome is also available via http://ggkbase.berkeley.edu/Forterrea/organisms (last accessed March 23, 2018). The mapped read file can also be downloaded from this site under associated files.
Present address: Department of Chemistry, Group for Aquatic Microbial Ecology (GAME), Biofilm Centre, University of Duisburg-Essen, Germany
Alexander J. Probst and Jillian F. Banfield contributed equally to this work.
ISSN:1759-6653
1759-6653
DOI:10.1093/gbe/evy067