Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales

Abstract

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

“…We observed a large number of bacterial taxa whose abundance was linked to tillage history, where tillage favored microbiomes with high community-weighted genome size and rrn copy number. Genome size is highly conserved across broad phylogenetic distances [84], lending support to our conclusions despite the fact community-weighted traits were inferred from reference genomes and at low phylogenetic resolution for many taxa. Future research is needed to confirm these observations using shotgun metagenomic approaches.…”

Linking prokaryotic genome size variation to metabolic potential and environment

“…However, it is important to remark that DNA extraction, assembly, binning and/or quality check of aquatic cyanobacterial MAGs is still a big challenge that needs to be addressed ( Supplementary Material 3 ) (Alvarenga et al, 2017; Kim Tiam et al, 2019). All in all, these results support that both environment (Rodríguez-Gijón et al, 2022) and taxonomy (Martinez-Gutierrez and Aylward, 2022) impact on existent pelagic genome size distributions.…”

“…Over the last two decades, different explanations have been postulated to find the mechanisms responsible for the variations in prokaryotic genome length. Reported drivers of genome size are phylogenetic history (Biller et al, 2015;Martinez-Gutierrez and Aylward, 2022), lifestyle such as freeliving, particle attached or host-associated (Giovannoni et al, 2014;Moran and Mira, 2001;van Ham et al, 2003), or environment such as marine, freshwater, different types of sediments or different hosts in host-associated microorganisms (Rodríguez-Gijón et al, 2022;Simonsen, 2022). While many factors have been found to partially explain genome size, ultimately, this implies that multiple evolutionary forces and their interactions shape genome size in prokaryotes.…”

Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria

“…The kappa (κ) and delta ( δ ) were also estimated using the Geiger package. A high value of K represents punctuated evolution, and a high value of δ (>1) represents accelerated evolution ( 88 ). Moreover, phylogenetically independent contrasts were computed on the genomic GC data and the genome-pathway matrix to test the variation pattern of DRR without phylogenetic influence using the ape package.…”