Evolution of genome architecture - PubMed (original) (raw)
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Evolution of genome architecture
Eugene V Koonin. Int J Biochem Cell Biol. 2009 Feb.
Abstract
Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome architectures are, mostly, products of neutral processes or epiphenomena of more general selective processes, such as selection for genome streamlining in successful lineages with large populations. Selection for specific gene arrangements (elements of genome architecture) seems only to modulate the results of these processes.
Figures
Figure 1
The distinct genome architectures of prokaryotes, unicellular eukaryotes and multicellular eukaryotes. Genes are shown by rectangles with the arrowhead indicating the direction of transcription. Exons are shown by rectangles without arrowheads. Intergenic regions are shown by straight lines, and introns are shown by squiggly lines. The schematic is not to scale.
Figure 2
Genome size versus the number of protein-coding genes for selected organisms from different divisions of life. The plot is on a semi-logarithmic scale. Black squares, large DNA viruses; green diamonds, bacteria; red diamonds, archaea; blue circles, unicellular eukaryotes (including fungi); orange circles, multicellular eukaryotes (plants and animals). The data were from the NCBI Genome Project database (NCBI Genomes 2008).
Figure 3
Comparison of gene orders in prokaryotic genomes. In the genomic dot-plots, each point corresponds to a pair of orthologous genes identified as bidirectional best hits in BLASTP comparisons of the complete sets of protein sequences encoded in the corresponding genomes (Tatusov et al., 1997). (a) nearly complete colinearity with a few breakpoints: Borrelia afzelii strain PKo vs B. burgdorferi starin B31. (b) moderate genome rearrangement in bacteria, X-shaped pattern indicative of inversion around the origin of replication: Xanthomonas axonopodis pv. citri strain 306 vs X. campestris pv. campestris strain 8004. (c) moderate genome rearrangement in bacteria, X-shaped pattern indicative of inversion around the origin of replication: Pyrococcus horikoshii OT3 vs P. abyssi GE5 (d) Extensive genome rearrangement in bacteria: Streptococcus gordonii str. Challis substrain CH1vs S. pneumoniae D39.
Figure 4
The evolutionary forces affecting genome architecture
References
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