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Comput Struct Biotechnol J. 2019 Mar 7;17:362-370. doi: 10.1016/j.csbj.2019.03.001. eCollection 2019.

Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals.

Author information

1
Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.
2
Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.
3
Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway.
4
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.
5
Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
6
Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden.

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.

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