Genomes in flux: The evolution of archaeal and proteobacterial gene content

Item Type:	Article
Title:	Genomes in flux: The evolution of archaeal and proteobacterial gene content
Creators Name:	Snel, B. and Bork, P. and Huynen, M.A.
Abstract:	In the course of evolution, genomes are shaped by processes like gene loss, gene duplication, horizontal gene transfer, and gene genesis (the de novo origin of genes). Here we reconstruct the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes. We estimate that the ancestor of the Proteobacteria contained around 2500 genes, and the ancestor of the Archaea around 2050 genes. Although it is necessary to invoke horizontal gene transfer to explain the content of present day genomes, gene loss, gene genesis, and simple vertical inheritance are quantitatively the most dominant processes in shaping the genome. Together they result in a turnover of gene content such that even the lineage leading from the ancestor of the Proteobacteria to the relatively large genome of Escherichia coli has lost at least 950 genes. Gene loss, unlike the other processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection.
Keywords:	Amino Acid Substitution, Archaea, Archaeal Genes, Archaeal Genome, Bacteria, Bacterial Genes, Bacterial Genome, Gene Deletion, Gene Duplication, Genetic Models, Genetic Recombination, Horizontal Gene Transfer, Molecular Evolution, Mutagenesis, Phylogeny, Proteobacteria
Source:	Genome Research
ISSN:	1088-9051
Publisher:	Cold Spring Harbor Laboratory Press
Volume:	12
Number:	1
Page Range:	17-25
Date:	1 January 2002
Official Publication:	https://doi.org/10.1101/gr.176501
PubMed:	View item in PubMed

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