Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

By Eugene V. Koonin, Yuri I. Wolf. Nucleic Acids Research, 2008

701 citations recorded by the source corpus.

The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/631aed33530c24035a07c43128c70e89410489ed

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Citations in the corpus

Mechanisms of Microbial Carbon Sequestration in the Ocean - Future Research Directions (2014, background): “Another problem is that not all of the genes in even heavily studied organisms, such asE cherichia coli,are completely known, and typically 10–20 % of a prokaryotic genome will not be similar to genes from any organism (Koonin and Wolf, 2008).”
Implications of streamlining theory for microbial ecology (2014, background): “…different from unimodality (see Supplementary Methods), including all ‘Finished’, ‘Permanent Draft’ and ‘Draft’ genomes supports the trend observed by Koonin and Wolf (2008); (Hartigan’s Dip Test (Hartigan and Hartigan, 1985), N¼ 5689, D¼ 0.01, P¼ 7.56 10 5), with separation into two…”
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis (2013, methodology): “pl can be used to report cloud, shell, soft-core, and core clusters (24) and to display them graphically (if R is installed), as shown in Fig.”
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales (2015, background): “can be decomposed into three distinct components: the small core of (nearly) universal genes, the much larger “shell” of moderately conserved genes, and the large, incompletely defined “cloud” of rare genes [53].”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “coli revealed that up to 30% of genes in pathogenic strains were acquired by HGT often creating duplication events and modifying metabolic networks by adding operons that encode two or more enzymes [253].”
Microbial communities and their relevance for ecosystem models: Decomposition as a case study (2010, background): “Thus, an important direction for future research is determining the identity of functional genes, assessing which functional processes are evolutionarily constrained (Koonin and Wolf, 2008), and which traits are correlated.”
Grammar of protein domain architectures (2019, background): “This trend is not surprising because archaeal genomes are typically smaller in size and encode fewer domain families than bacterial, let alone eukaryotic genomes (67).”
The ecological coherence of high bacterial taxonomic ranks (2010, background): “However, genomic signatures of more complex phenotypes such as virulence, thermophily or radiation resistance have been more difficult to delineat”