Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
Highlights
In prokaryotes and eukaryotes, the genome consists of one or several DNA molecules that contain the genetic information of the organism
We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while GC-biased gene conversion (gBGC) and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes
Genomic evolution in eukaryotes can have taken a very different route than what has currently been observed for prokaryotes [126]; while base composition evolution in prokaryotes is tightly associated with natural selection mediated by the environment, selective neutral processes, such as gBGC, linked to cross-over recombination could be one mechanism moulding base composition in eukaryotes
Summary
The genome consists of one or several DNA molecules that contain the genetic information of the organism. While all prokaryotes and eukaryotes have genomes consisting exclusively of DNA molecules some viruses have, in addition to single and double stranded DNA genomes, RNA genomes that are either single or double stranded [1]. Genomes are dynamic in the sense that offspring evolve through mutation, or recombination. Genomes change either due to mutation of bases (e.g. C changes to T during replication), loss of long or short stretches of nucleotides (including genes), replication of (oligo-) nucleotides, rearrangements due to for instance, transposons, recombination, duplication, transformation, conjugation and/or transduction [2,3]
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