Metrics of Genomic Complexity in the Evolution of Bacterial Endosymbiosis

Abstract

Endosymbiosis can be considered a regressive or degenerative evolutionary process characterized at the genomic level by genome erosion and degeneration due to high mutational pressure toward AT (adenine and thymine) bases. The genomic and biological complexity of endosymbionts must be lower than that of the free-living bacteria from which they evolved. In the present work, we contrasted whether two proposed metrics for measuring genomic complexity in both types of bacteria, GS and BB, reflect their complexity, expecting higher values in free-living bacteria than in endosymbionts. On the other hand, we endeavored to delve into the factors that contribute to the reduction in metric values in endosymbionts, as well as their eventual relationship with six genomic parameters associated with functionality. This study aimed to test the robustness of these proposed metrics in a well-known biological scenario, such as the endosymbiosis process.

Keywords: complexity metrics; endosymbiosis; genomic complexity.

Figure 1

The phylogenetic tree used a concatenated alignment of 27 conserved protein domains. It was inferred using IQ-TREE v2.1.3 under the LG + F + I + G4 model with 4000 ultrafast bootstrap replicates. Dots in branches show support values according to the legend. Species whose names are colored red are endosymbionts, and those in black are free-living. The endosymbionts marked with a red square are facultative, while the rest are obligate.

Figure 2

Boxplots of each trait for free-living and endosymbiont genomes in the whole tree. Stars indicate the statistical significance of the mean based on the phylogenetically informed test.

Figure 3

Phylogenetic correlation plots for (a) the whole tree, (b) the Enterobacterales, (c) the Oceanospirillales, and (d) the Bacteroidota clades. Crosses indicate statistically non-significant correlation values, and the correlation value is shown in color according to the legend.

Figure 4

Phylogenetic-informed principal component analysis (PCA) of (a) the entire tree, (b) Enterobacterales, (c) Oceanospirillales, and (d) Bacteroidota clade. Arrows show the loadings for each variable, and the points represent the genomes; their color shows the lifestyle of the organisms according to the legend.

Figure 5

Plot representing the values of Genomic Signature against GC content. Values in red correspond to endosymbionts, while values in blue correspond to the free-living organisms.

Figure 6

Plot representing the values of BB against the percentage of hapaxes. Values in red correspond to endosymbionts, while values in blue correspond to the free-living organisms.