Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
Touchon
Marie
M
Atelier de BioInformatique, Université Pierre et Marie Curie--Paris 6, Paris, France.
Hoede
Claire
C
Tenaillon
Olivier
O
Barbe
Valérie
V
Baeriswyl
Simon
S
Bidet
Philippe
P
Bingen
Edouard
E
Bonacorsi
Stéphane
S
Bouchier
Christiane
C
Bouvet
Odile
O
Calteau
Alexandra
A
Chiapello
Hélène
H
Clermont
Olivier
O
Cruveiller
Stéphane
S
Danchin
Antoine
A
Diard
Médéric
M
Dossat
Carole
C
Karoui
Meriem El
ME
Frapy
Eric
E
Garry
Louis
L
Ghigo
Jean Marc
JM
Gilles
Anne Marie
AM
Johnson
James
J
Le Bouguénec
Chantal
C
Lescat
Mathilde
M
Mangenot
Sophie
S
Martinez-Jéhanne
Vanessa
V
Matic
Ivan
I
Nassif
Xavier
X
Oztas
Sophie
S
Petit
Marie Agnès
MA
Pichon
Christophe
C
Rouy
Zoé
Z
Ruf
Claude Saint
CS
Schneider
Dominique
D
Tourret
Jérôme
J
Vacherie
Benoit
B
Vallenet
David
D
Médigue
Claudine
C
Rocha
Eduardo P C
EP
Denamur
Erick
E
D004251:DNA Transposable Elements; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D005823:Genetics; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics; D016013:Likelihood Functions; D008954:Models, Biological; D008957:Models, Genetic; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic
D004251:DNA Transposable Elements