Published online before print
December 14, 2001, 10.1101/gr.176501
Vol. 12, Issue 1, 17-25, January 2002
Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content
Berend
Snel,1,3
Peer
Bork,1,2 and
Martijn A.
Huynen1,2
1 European Molecular Biology Laboratory, 69117 Heidelberg,
Germany; 2 Max-Delbrück-Centrum for Molecular Medicine,
13122 Berlin-Buch, Germany
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.
3
Corresponding author.
12:17-25 ©2002 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/02 $5.00
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