Driven progressive evolution of genome sequence complexity in Cyanobacteria

Abstract

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor–descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.

Evolutionary Pathways and Trajectories in Antibiotic Resistance

“…Evolution not only creates entities of higher hierarchical levels (such as eukaryotic cells, plants animals), thereby making it more complex, it also produces complexity inside individual entities. The diversification inside each family of ARGs (generation of orthologs) and inside each bacterial clone of a single species is also a process of complexification, which increases the number of genes (143,1270) and, in the jargon of genome complexity metrics, sequences of length K (k-mers) (1271). The important issue is whether such an increase in endo-diversity under antibiotic exposure, which facilitates the emergence of novel genetic associations and epistatic bonds, is fostering more evolvability or evolutionary energy (1272).…”

A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium

“…We selected 75 ortholog sequences from morphological and ecologically diverse cyanobacterial strains for phylogenetic analysis to investigate the relationship of hltA orthologs across cyanobacteria. The distribution of the resulting hltA tree topology maintained a high degree of similarity with the core cyanobacterial phylogeny ( 31 – 33 ) shown by the preservation of distinct clades A–H ( Fig. 4A and Fig.…”

The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS-CoV-2 coronavirus

“…Here we show that, despite its short length (29,912 bp for the reference genome) and the short time-lapse analyzed (28 months), the coronavirus RNA genomes can be divided into 4-9 compositional domains (~0.27 segments by kbp on average). Although such segment density is lower than in free-living organisms, like cyanobacteria where we observed an average density of 0.47 segments by kbp (Moya et al, 2020), it may suffice for comparative evolutionary analyses of compositional sequence heterogeneity in these genomes, which might shed light on the origin and evolution of the COVID-19 pandemic.…”

“…To this end, we computed the Sequence Compositional Complexity, or SCC (Román-Roldán et al, 1998), an entropic measure of genome heterogeneity, meant as the number of domains and nucleotide differences among them, identified in a genome sequence through a proper segmentation algorithm (Bernaola-Galván et al, 1996). By using phylogenetic ridge regression, a method that has been able to reveal evolutionary trends in both macro- (Melchionna et al, 2019;Serio et al, 2019) and micro-organisms (Moya et al, 2020), we present here evidence for a long-term tendency of decreasing genome sequence heterogeneity in SARS-CoV-2. The trend is shared by the virus most important Variants of Concern (VoCs), Alpha or Delta, and greatly accelerated by the recent rise to dominance of Omicron (Du et al, 2022).…”