RESEARCH ARTICLE

GC-Content Evolution in Bacterial Genomes:

The Biased Gene Conversion Hypothesis
Expands
Florent Lassalle1,2,3,4,5,6, Séverine Périan1,2,3, Thomas Bataillon7, Xavier Nesme1,2,4,5,
Laurent Duret1,2,3, Vincent Daubin1,2,3*
1 Université de Lyon, Lyon, France, 2 Université Lyon 1, Villeurbanne, France, 3 CNRS, UMR 5558,
Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France, 4 CNRS, UMR 5557, Ecologie
Microbienne, Villeurbanne, France, 5 INRA, USC 1364, Ecologie Microbienne, Villeurbanne, France,
6 Ecole Normale Supérieure de Lyon, Lyon, France, 7 Aarhus University, Bioinformatics Research Center,
Århus, Denmark

* Vincent.daubin@univ-lyon1.fr

Abstract
OPEN ACCESS

Citation: Lassalle F, Périan S, Bataillon T, Nesme X,

The characterization of functional elements in genomes relies on the identification of the
Duret L, Daubin V (2015) GC-Content Evolution in footprints of natural selection. In this quest, taking into account neutral evolutionary pro-
Bacterial Genomes: The Biased Gene Conversion cesses such as mutation and genetic drift is crucial because these forces can generate pat-
Hypothesis Expands. PLoS Genet 11(2): e1004941.
terns that may obscure or mimic signatures of selection. In mammals, and probably in many
doi:10.1371/journal.pgen.1004941
eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC)
Editor: Dmitri A. Petrov, Stanford University, UNITED
has been documented. This mechanism generates patterns identical to what is expected
STATES
under selection for higher GC-content, specifically in highly recombining genomic regions.
Received: May 16, 2014
Recent results have suggested that a mysterious selective force favouring higher GC-
Accepted: December 8, 2014 content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here,
Published: February 6, 2015 we show that gBGC is probably at work in most if not all bacterial species. First we find a
Copyright: © 2015 Lassalle et al. This is an open
consistent positive relationship between the GC-content of a gene and evidence of intra-
access article distributed under the terms of the genic recombination throughout a broad spectrum of bacterial clades. Second, we show
Creative Commons Attribution License, which permits that the evolutionary force responsible for this pattern is acting independently from selection
unrestricted use, distribution, and reproduction in any
on codon usage, and could potentially interfere with selection in favor of optimal AU-ending
medium, provided the original author and source are
credited. codons. A comparison with data from human populations shows that the intensity of gBGC
in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is
Data Availability Statement: All genomic data are
available from the HOGENOM database (http://pbil. not restricted to sexual Eukaryotes but also widespread among Bacteria and could there-
univ-lyon1.fr/databases/hogenom/home.php) All other fore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria,
relevant data are within the paper and its Supporting it can account for previously unexplained observations, such as the apparent non-equilibri-
information files.
um of base substitution patterns and the heterogeneity of gene composition within bacterial
Funding: This work was supported by French genomes. Because gBGC produces patterns similar to positive selection, it is essential to
National Research Agency (ANR) grant Ancestrome
take this process into account when studying the evolutionary forces at work in
(ANR-10-BINF-01-01) and EcoGenome (BLAN-08-
0090). (http://www.agence-nationale-recherche.fr/). bacterial genomes.
FL received a doctoral scholarship from Ecole
Normale Supérieure de Lyon (http://www.ens-lyon.eu/
) and is supported by ERC grant BIG_IDEA 260801
(http://erc.europa.eu). The funders had no role in

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 1 / 20

 Recombination Drives the Bacterial Genome Landscape

study design, data collection and analysis, decision to

publish, or preparation of the manuscript. Author Summary
Competing Interests: The authors have declared Classical population genetics models indicate that the efficiency of selection, and hence ad-
that no competing interests exist.
aptation, depends on a number of non-selective factors, such as the size of a population or
the intensity of recombination. In the last 10 years, evidence has accumulated that another
mechanism called GC-Biased Gene Conversion (gBGC) can interfere with selection and
even mimic its effects. This phenomenon, which arises from a particularity of the recombi-
nation machinery, was first thought to be restricted to sexual eukaryotic organisms. Here,
we show that this mechanism probably exists in Bacteria and has a strong impact on their
genome evolution. This discovery not only explains many previously unconnected features
of bacterial genome evolution, but also highlights the importance of non-adaptive evolu-
tionary processes in Bacteria.

Introduction
Comparative genomics is a fundamental key to the inner workings of genomes. The identifica-
tion of genes and other functional elements such as regulatory regions, as well as the under-
standing of their influence on the fitness of organisms rely essentially on the detection of
signatures of natural selection within genomes [1]. In that respect, devising a model of se-
quence evolution in the absence of selective constraints (a neutral model) is critical for the de-
tection of functional sequences. Indeed, to explain the features of a given genomic segment,
comparing the fit of a neutral model to that of a model that also invokes selection (either puri-
fying or positive) is the operational way to infer evolutionary constraint and hence function.
The base composition of genomic sequences varies widely, both across species and along
chromosomes [2,3]. For instance, the genomic GC-content of cellular organisms ranges from
13% to about 75% [4,5], with vast intra-genomic heterogeneity. These large-scale variations in
base composition affect all parts of genomes, intergenic regions and genes—including all three
codon positions [6]—and hence cannot be simply explained by selective constraints on the en-
coded proteins. Determining the underlying causes (selective or neutral) of these variations
in GC-content is a major issue in genetics: if they result from selection, it implies that the geno-
mic base composition per se is an important trait that contributes to the fitness of organisms;
conversely, if these “genomic landscapes” are largely shaped by non-adaptive molecular pro-
cesses, then characterizing these processes is essential for the reliable detection of selection (see
e.g. [7]).
In mammals, the analysis of polymorphism data and substitution patterns along genomes
demonstrated that the evolution of GC-content is driven by recombination, which tends to
increase the probability of fixation of AT!GC mutations [8,9]. The impact of recombination
on base composition in these genomes is most probably due to a phenomenon known as GC-
biased gene conversion (gBGC), which favours G/C nucleotides at polymorphic sites in the
conversion of intermediates of recombination (see review in [10]). Although gBGC as a process
is unrelated to natural selection, it affects the probability of fixation of alleles in patterns similar
to selection [11]. It has been shown to be an important confounding factor, which can mimic
some marks of positive selection [7,12] and interfere with selection by actively promoting the
fixation of deleterious alleles [13,14]. The process of gBGC has been observed directly in meio-
sis products from yeast and human [15,16], and there is ample evidence, based on the analysis
of relationships between recombination rate and substitution patterns within genomes, that
this process affects many other eukaryotes [17–19].

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 Recombination Drives the Bacterial Genome Landscape

In Bacteria and Archaea, several environmental factors potentially affecting genomic GC-
content have been proposed (such as the availability of oxygen or nitrogen in the environment,
growth temperature, or the variety of environments encountered by an organism, see for in-
stance [20] and ref. therein). Because these effects are weak and the nature of the selective pres-
sures remain elusive, the major force driving genomic GC-content has long been considered to
be mutational bias [21]. Recently however, two independent analyses have shown that in virtu-
ally all Bacteria, independently of their genomic GC-content, there is an excess of G/C!A/T
mutations [22,23]. This suggests that an unknown process, selective or neutral, is opposing this
universal mutational bias by favouring the fixation of G/C alleles Previously, an analysis of a
large number of E. coli genomes had suggested a possible role of gBGC, based on the link be-
tween GC-content, recombination and the organization of the chromosome in this species
[24]. However Hildebrand et al. [23] observed that the excess of G/C!A/T mutations was still
present after removing datasets with evidence of recombination. Moreover they found no cor-
relation between GC-content and recombination rate across bacterial species. They therefore
concluded that this force could not be gBGC and hence that selection was driving an increase
of genomic GC in Bacteria. The nature of this selective advantage remains however mysterious,
though various hypotheses have been proposed [25,26].
Here we argue that the analyses performed by Hildebrand et al. [23] are not conclusive re-
garding the gBGC hypothesis, and we present evidence that variations in GC-content observed
in Bacteria are influenced by gBGC. One pervasive signature of gBGC is that genomic regions
undergoing high recombination rates will also acquire a high GC-content [6]. We thus studied
the relationship between recombination and GC-content in 20 groups of Bacteria and one
group of Archaea. This dataset covers a wide range of clades representative of the bacterial di-
versity. To avoid problems inherent to comparisons of recombination rates among species
(such as differences in polymorphism, genome samples, population size, mutation rates, an
other life history factors), we examined the intragenomic variability for both recombination
and GC-content.
We show that in a wide variety of bacterial species, genes with evidence of recombination
have a higher GC-content. We further show that this bias towards G/C nucleotides in recom-
bining genes cannot be explained by selection on codon usage, and could interfere with the se-
lection for AT-ending optimal codons. These two observations strongly suggest that
homologous recombination, via gBGC, is a crucial factor universally influencing the nucleotide
content of genes and genomes. If confirmed, gBGC can account for several pervasive yet unex-
plained features of bacterial genomes. Finally, we emphasize that because gBGC has the ability
to both mimic and interfere with natural selection, gBGC must be considered by future studies
geared at understanding processes driving bacterial genome evolution.

Results
A universal relationship between recombination and GC% in Bacteria
In Bacteria, recombination occurs in the form of gene conversion (i.e. unidirectional transfer of
genetic material from a donor sequence towards a homologous recipient sequence). To detect
past gene conversion events in bacterial species, it is necessary to compare closely related ge-
nomes. We therefore selected in the database of homologous gene families HOGENOM (re-
lease 6) [27] all groups of closely related species or strains encompassing at least 6 sequenced
genomes. This dataset contains 20 bacterial groups and one archaeal group. For each gene fam-
ily represented in these groups, we computed i) the average GC-content at different positions
of codons and ii) the index of recombination provided by PHI [28] based on alignments of
standardized length (see methods for details). PHI is a rapid method for detecting

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 Recombination Drives the Bacterial Genome Landscape

recombination in multiple alignments at the scale of the gene, which has been shown to be
more robust than most methods to variations in recombination rates, sequence divergence and
population dynamics [28]. We used this test to determine if homologous gene families had ex-
perienced gene conversion events among members of the taxa of interest. One important fea-
ture of this test is that it measures whether there is sufficient phylogenetic signal in an
alignment to tell if recombination has occurred. Only alignments with sufficient signal, wheth-
er recombinant or non-recombinant were retained for tests in the remaining of this study. We
also used three other approaches for detecting recombination, and these confirm the robust-
ness of our conclusions (see Methods and Supplementary Material).
In Eukaryotes, a general relationship between various estimates of recombination rate and
the GC% of genes has been documented and provides indirect evidence for gBGC. Our first
goal was to test this prediction in Bacteria and Archaea. To exclude a potential effect of the
number of genes in the alignment on our estimates of recombination (because alignments with
more sequences are expected to give more power to detect recombination), we focused on sin-
gle-copy genes of the core genome (i.e. genes that are present in only one copy and found in
each genome of a group). In 7 of the 21 groups, the proportion of single-copy genes of the core
genome with evidence for recombination was very low (<2% of all gene alignments tested),
suggesting that these species are clonal or nearly so (Table 1; shaded datasets in Fig. 1). Indeed,
the Burkholderia pseudomalei group, Chlamydia trachomatis, Francisella tularensis, Mycobac-
terium tuberculosis and Yersinia pestis are species known to be pathogenic clonal complexes
with low polymorphism and probably very low recombination [29–33], while Brucella spp. and
Sulfolobus spp. are likely composed of ecologically isolated clades, because of their respective
lifestyle as obligate intracellular pathogen or ecotypes endemic of hot springs [34–36]. In 11 of
the 14 remaining groups, we found a significant positive difference in average GC-content at
all and/or at the third position of codons (GC3) between recombinant and non-recombinant
genes (Fig. 1). In these 11 species, the difference in GC3 is always larger than that at all posi-
tions, suggesting that the effect of recombination on gene composition is stronger at synony-
mous positions (probably because of purifying selection on protein sequences). Two notable
exception to this pattern are i) the bacterial species Helicobacter pylori, where GC-content
seems to be lower in recombining genes and ii) the Bacillus anthracis/cereus group, where GC
at all positions and GC3 display opposite patterns, with GC3 being higher in recombining
genes. Consistent results are obtained using alternative recombination detection methods
(S1 Fig.).

Selection on optimal codons cannot explain the association of GC with

recombination
Recombination is known to enhance the efficacy of selection by breaking linkage between
neighboring selected sites. It is therefore possible that selection is more efficient in recombining
genes. This effect (referred to as Hill-Robertson interference) should theoretically be more
pronounced in the case of selection on codon usage [37], which is relatively weak compared to
selection on amino acid sequences. Thus recombination—in the absence of any gBGC—can
potentially explain the pronounced effect observed on GC3: if Hill-Robertson interference
leads to a higher frequency of optimal codons in highly recombining genes, and if optimal co-
dons tended to be GC-rich, this effect could explain a relationship between GC-content and
recombination. The “selection model” sketched above predicts that the frequency of all optimal
codons (both GC-ending and AU-ending) should increase with recombination. In contrast, a
model incorporating the effect of gBGC predicts that GC-ending codons (not specifically opti-
mal codons) should be enriched in recombining regions, and that AU-ending codons (and

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 Recombination Drives the Bacterial Genome Landscape

Table 1. Dataset used in this study.

Dataset Taxon name Nb. of Total Nb. of Nb. of Nb. of non- Nb. of Mean Mean Mean Mean
genomes nb. of core recombinant recombinant unclassified GC of GC3 of GC of GC3 of
core genes core genes core genes core genes* core core core core
genes of size genes genes genes genes
 (%) (%) of size of size
900bp  
900bp 900bp
(%) (%)
Brsp Brucella spp. 9 1675 776 0 422 354 58,1 67,3 58,8 68,6
Ftul Francisella 8 1015 469 0 359 110 33,3 21,8 33,8 21,9
tularensis
Mtub Mycobacterium 7 2222 1078 0 91 987 65,6 79,3 66,1 80,3
tuberculosis
complex
Bmal Burkholderia 9 1482 781 4 628 149 67,9 88,3 68,7 89,7
Pseudomallei
group
Ypes Yersinia pestis 11 2017 1073 7 679 387 48,7 48,9 49,3 49,9
Ctra Clamydia 13 772 391 6 376 9 41,6 34,6 41,8 34,6
trachomatis
Susp Sulfolobus spp. 8 1386 547 8 465 74 34,7 29,1 35,4 29,2
Bcen Burkholderia 8 1939 936 106 829 1 67,4 87,4 68,2 89,1
cenocepacia
complex (BCC)
Saur Staphylococcus 15 1464 668 92 571 5 33,5 22,4 34,2 22,2
aureus
Blon Bifidobacterium 6 1006 600 73 358 169 61,3 77,2 61,9 78,2
longum
Abau Acinetobacter 6 1429 638 115 516 7 40,3 29,9 40,8 30,2
spp.
Cjej Campylobacter 6 1048 501 93 403 5 31,0 19,4 31,6 19,6
jejunii
Cbot Clostridium 8 1715 730 168 562 0 28,6 16,8 29,1 16,4
botulinum
Spyo Streptococcus 12 1051 496 119 370 7 38,9 31,6 39,6 32,2
pyogenes
Spne Streptococcus 13 1090 507 119 368 20 41,3 36,9 42,0 37,4
pneumoniae
Sent Salmonella 14 2121 975 323 652 0 53,4 59,4 54,6 61,6
enterica
Lisp Listeria spp. 8 1631 678 328 350 0 38,1 29,6 38,8 29,5
Bant Bacillus 17 1730 727 422 305 0 36,3 26,3 37,0 26,5
anthracis/cereus
group
Nmen Nesseiria 8 1156 552 339 213 0 54,4 63,9 55,3 65,7
meningitidis
Ecol Escherichia coli 35 1357 619 442 177 0 52,3 56,3 53,3 58,0
Hpyl Helicobacter 14 995 467 334 133 0 39,9 42,8 40,4 43,3
pylori

Total number of genes in the core-genome, as well as the number of core genes classified as recombinant and non-recombinant based on PHI analysis
and unclassified ones (genes with insufficient signal to test for recombination, excluded from comparison tests) are indicated. The mean proportion of GC
(all positions of codons) and GC3 (third position of codons) of core genes are shown for each dataset.

doi:10.1371/journal.pgen.1004941.t001

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 Recombination Drives the Bacterial Genome Landscape

Figure 1. Effect of recombination on core genes GC-content. Difference in average GC-content of

recombinant and non-recombinant genes, measured on entire CDS length (GC, dark brown) or at third codon
position only (GC3, light brown) in the core genome of each dataset. Recombinant status was determined
using the PHI test [28] (p < 0.05) on alignments of core gene families trimmed to a common length of 900bp.
A positive difference indicates that recombinant families are enriched in GC. Stars indicate the level of
significance of a Student’s t-test (“*”, p < 0.05; “**”, p < 0.01; “***”, p < 0.001). Statistical tests are detailed
further in S1 Table. Dataset abbreviations are explained in Table 1. Figures next to dataset names indicate
the number of recombinant core gene families in the dataset, figures in parenthesis indicate their percentage
in the total pool of recombinant and non-recombinant families. Colored boxes on the right indicate the mean
percentage of GC and GC3 values of core genes. Shading in background marks datasets with less than 20
recombinant gene families (detailed Table 1).
doi:10.1371/journal.pgen.1004941.g001

possibly AU-ending optimal codons if gBGC is strong enough to override selection on codon
usage) should display the opposite pattern. We therefore looked specifically at the frequency of
the different types of codons, i.e. optimal and non-optimal, in recombining and non-
recombining genes.
There is a debate over the best way to define optimal codons, based on their over-representation
in either ribosomal protein genes (RP), or genes with the highest codon bias (HCB) [38–40].
We therefore analyzed the frequency of GC-ending and AU-ending optimal codons (FopGC
and FopAU) and non-optimal codons (FnopGC and FnopAU) according to both RP and HCB
definitions (Fig. 2, S3 Fig., and S4 Fig., respectively). The higher GC3 of recombining genes
means that GC-ending codons are over-represented in recombining genes, but this is true for
optimal GC-ending codons in only 2 (RP optimal codons) or 4 (HCB optimal codons) species
out of 11. This effect is hence essentially due to non-optimal codons (FnopGC is significantly
higher in recombining genes than non-recombining genes in respectively 9 and 8 species for
RP and HCB definitions). Moreover, optimal AU-ending codons are significantly depleted in
recombining genes for 8 (resp. 5) species for RP (resp. HCB) codons. In fact, only two species,
S. pyogenes and Nesseiria meningitidis (using the HCB method—only S. pyogenes using the RP
method) exhibit a pattern partially compatible with the selection hypothesis presented above.
All species display either an increase of FnopGC and/or a decrease of FopAU in recombining
genes, a fact that cannot be explained by a higher efficiency of selection. This pattern excludes
the possibility of pervasive selection for codon usage promoting a better adaptation to the pool
of tRNA for genes in regions of high recombination, but is compatible with the predictions of
gBGC.

Intergenic regions display a pattern that is consistent with gBGC

In principle, gBGC should affect all genomic regions where recombination occurs, including
intergenic regions. Intergenes are generally shorter than coding regions. Furthermore, they
evolve more rapidly and hence are more difficult to align. Hence, the methods that we used to
detect recombination in coding regions cannot be applied with intergenes. We therefore used
the recombinant or non-recombinant status of the neighboring protein-coding genes as a
proxy of the status of the intergenes. In 11 of the 14 taxonomic groups, we observed that inter-
genes flanked by recombining genes have a higher GC-content than intergenes flanked by non-
recombining genes (S2 Fig.). The difference in GC-content between the two classes is weaker
than that observed in coding regions, and when considered individually, only one comparison
is statistically significant (Streptococcus pyogenes, p < 0.01). This is possibly because the predic-
tion of recombination status of intergenic regions is indirect (based on the status of flanking
genes) and therefore less accurate than that of coding regions. However, the number of cases
where the difference in GC-content between the two classes is positive (11 out of 14 compari-
sons) is significantly higher than expected by chance (Chi-squared test: p = 0.03).

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 Recombination Drives the Bacterial Genome Landscape

Figure 2. Effect of recombination on codon usage of core genes. Difference in frequency of optimal (fop)
or non-optimal (fnop) codons (as determined by RP method) in recombining and non-recombining genes in
each dataset for AU-ending (redish colors) and GC-ending (blueish colors) codons. The recombination status
of genes was determined as in Fig. 1, only datasets with more than 10% recombining genes are shown. A
positive difference indicates that recombining genes are enriched in a category of codons, while a negative
difference indicate depletion. Stars indicate significance of a Student’s t-test between recombining and non
recombining genes. Colored boxes on the right of dataset names indicate the numbers of AU-ending and GC-
ending optimal or non-optimal codons used by the taxon (detailed in S2 Table). Symbols and dataset
abbreviations as in Fig. 1; shading is only used to distinguish between datasets. It should be noticed that
variations in fopGC and fnopAU (resp. fopAU and fnopGC) are not totally independent (typically, for all
amino-acids encoded by two synonymous codons, if the optimal codon is GC ending, the non-optimal is AT-
ending).
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 Recombination Drives the Bacterial Genome Landscape

Quantifying the impact of recombination on bacterial genome evolution

To quantify the relationship between recombination and base composition, we first analyzed
the genome of S. pyogenes, one of the species for which the signature of gBGC is strong (Fig. 1,
see also Sup. Mat.). We used ClonalOrigin [41] to compute the population-scaled recombina-
tion rate (rho) for each gene of the core genome. The correlation between rho and the GC-
content at third codon position of each gene (GC3) is slight but significant (R2 = 0.034,
p<10−4, n = 478). Interestingly, when we exclude genes for which the estimate of rho is less
reliable (about 10% of the data, see Sup. Mat.), the correlation strongly increases (R2 = 0.087;
p<10−9, n = 437). Due to the low amount of data available in a gene-scale alignment, the mea-
sure of rho is expected to be noisy. Thus, the observed correlation is probably an underestimate.
To try to get more robust estimates of rho, we binned the dataset into 20 groups of genes ac-
cording to their GC3, and we computed the correlation between the average GC3 and the aver-
age rho of each bin. Using this approach, we observed a strong correlation between the GC3
and recombination (R2 = 0.60; Fig. 3A).
For a comparison, we performed a similar analysis in humans: we randomly selected 600
human genes (which corresponds to the average number of genes analyzed in our bacterial
data sets), binned the data set into 20 groups of genes according to their GC3, and we comput-
ed the correlation between the average GC3 and the average recombination rate as obtained
from population-wide surveys [42]. The average correlation (computed after repeating the ran-
dom sampling 1,000 times) is R2 = 0.55 (with 95% of the R2 values in the interval [0.26–0.78];
one representative example is presented in Fig 3A).
Using this binning approach, we noted that the proportion of genes in a bin that are detected
as recombinant by PHI is strongly correlated with the average value of rho (R2 = 0.70; p<10−5).
This suggests that this index (hereafter referred to as PREC, for ‘proportion of recombinant’) is a
good proxy for the average recombination rate in a bin. In fact, we observed that GC3 correlates
more strongly with PREC (R2 = 0.68; Fig. 3B) than with rho. Given that the computation of rho
with ClonalOrigin is extremely time consuming, we decided to use PREC to evaluate the correla-
tion between GC3 and recombination rate in other species. Correlations were positive and signif-
icant for 11 of the 14 species, with R2 values ranging from 0.24 to 0.68, and we did not observe
any significant negative correlation (Fig. 3B). This shows that the correlations between GC-con-
tent and recombination rate in bacteria are of similar magnitude to what is observed in humans.

Discussion
The link between GC-content and recombination is independent from
constraints on protein coding genes
Our results suggest that recombination affects the GC-content of genes in most bacterial phyla.
We analyzed genes of the core genome to compare the base composition of genes with or with-
out evidence of recombination. In 11 of the 14 species in which a significant amount of recom-
bination could be detected, we observed that the GC-content (measured either at the third
codon position or along the entire coding region) is higher among recombining genes com-
pared to other (hereafter labeled as “non-recombining”) core genes.
Several hypotheses have been proposed to explain the variations in GC-content among bac-
terial genomes [25]. Several studies have revealed that the genomic GC-content of bacterial ge-
nomes is always higher than what would be predicted from mutational bias [22,23,43]. Hence,
it seems inescapable that some other evolutionary force is driving the genomic GC-content to-
wards higher values in virtually all bacterial species, except maybe for the most AT-rich ge-
nomes [22,43]. Recombination is known to enhance the efficiency of selection by breaking

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 Recombination Drives the Bacterial Genome Landscape

Figure 3. Correlations between GC3 and estimates of recombination rate. For each dataset, core genes are sorted by increasing GC3 and pooled into
20 classes of equal size. Correlations between the mean GC3 and mean recombination rate of each class are reported. (A) Correlation between GC3 and
coalescent-based estimates of recombination rate for Homo sapiens (Hsap) and Stretococcus pyogenes (Spyo). For Hsap, recombination rate is expressed
as cM∙Mb-1; a subset of 600 genes out of the 16,346 human genes is shown as a representative of 1,000 random samples (mean R2 is 55%, see Main Text).
For Spyo, recombination rate is expressed as the value of rho parameter in ClonalOrigin [41] inferences, which is scaled by arbitrary coalescent time units; a
subset of 437 genes out of 478 core genes was used, after removal of the 41 genes showing no convergence of the rho estimate (correlation on the full 478
core genes yields a R2 of 31%, see S1 Text). (B) Correlation between GC3 and PREC, the proportion of genes detected as recombinant by PHI test [28] in the
class, for all 14 bacterial datasets showing sufficient evidence of recombination (Table 1).
doi:10.1371/journal.pgen.1004941.g003

linkage among sites. It is therefore conceivable that our results merely reveal a universal selec-
tive pressure favoring GC-rich alleles. But the mechanism underlying such selection would
have to be acting more efficiently on synonymous sites than non-synonymous sites because the
difference of GC% between recombining and non-recombining genes is higher at the third po-
sition of codons. This excludes potential selection on amino-acid content. One selectable trait
that may influence synonymous positions is codon usage. If optimal codons tended to be GC-
rich, recombination could drive GC% higher by favoring the adaptation of genes to better

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 Recombination Drives the Bacterial Genome Landscape

translation efficiency. However, we observed a higher GC-content in recombining genes even

in species favoring A/U-ending codons (Fig. 2). Moreover, A/U-ending and G/C-ending co-
dons show opposite relationships with recombination in most species, irrespective of their op-
timality. These observations suggest that the evolutionary force explaining our results is also
largely independent from selection on codon usage. This conclusion is further supported by
the fact that the relationship between GC-content and recombination is also observed in inter-
genic regions (S2 Fig.).
In fact, as suggested by Hershberg and Petrov [22], who observed that the intergenic regions
of bacterial genomes also have higher GC% than expected from their mutational pattern, it
seems likely that the process is unlinked to gene expression or function. Hence, either there is
selection acting simultaneously on each nucleotide of a bacterial genome to become G or C, or
GC-biased gene conversion, which has now been observed in a variety of Eukaryotes is also at
work in Bacteria.

gBGC effect on nucleotide composition is manifest within genomes

The hypothesis that gBGC plays a role in bacterial genome evolution has been considered
previously [23]. Hildebrand et al. analyzed the correlation between genome-wide measures of
recombination rate (scaled by effective population size) with genomic GC-content among 34
species, covering different bacterial phyla. As they did not find any significant correlation, they
concluded that there was no evidence of gBGC in Bacteria [23]. However, we argue here that
this observation is not conclusive. In fact, the strength of gBGC depends on four variables: the
effective population size (Ne), the rate of recombination per bp per generation (r), the length of
conversion tracts (L) and the intensity of the repair bias (b0) (for review, see [6]). In a haploid
organism, the population-scaled gBGC coefficient is:
B¼2 Ne  r  L  b 0 ð1Þ

Similar to selection, the impact of gBGC on genome evolution depends on its intensity
relative to genetic drift, and becomes negligible when B  1. There is evidence that besides Ne
and r, both L and b0 can vary strongly across species. For example, in budding yeast, when a
GC/AT heterozygote site is involved in a gene conversion event, the GC-allele is transmitted
with a probability pGC = 0.507 (which is significantly higher than the expected Mendelian
transmission ratio; [15]), whereas in humans, a recent analysis of gene conversions tracts
associated to non-crossover recombination showed that GC-alleles are transmitted with a
probability pGC = 0.70 [16]. Thus, the parameter b0 (b0 = 2 ∙ pGC – 1) is about 30 times higher in
humans than in yeast. Conversely, gene conversion tracts are on average about 4 times longer
in yeast than in mammals [15,44]. Thus, for a same population-scaled recombination rate
(Ne r), the intensity of gBGC would be about 7 times stronger in humans than in yeast. This
example illustrates that because of variations in L and b0, the gBGC model does not necessarily
predict a good correlation between population-scaled recombination rate and GC-content
across species. In fact, to test the predictions of the gBGC model, it is more appropriate to in-
vestigate correlations between base composition and recombination rate within genomes, so
that the other parameters (Ne, L and b0) can be controlled for.

The impact of gBGC on bacterial genome evolution is quantitatively

strong
The observations presented previously are qualitatively consistent with the gBGC model. How-
ever, they do not provide a quantification of the impact of recombination on bacterial genomes:
to what extent might this model account for the strong variations of GC-content observed

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 11 / 20

 Recombination Drives the Bacterial Genome Landscape

across bacterial species? The gBGC model predicts that, all else being equal, the present-day
GC-content of a genome should directly reflect its average recombination rate over long
evolutionary time. To test this prediction, it is important to take into account two difficulties.
First, recombination rates measured in extant populations reflect recent events (more recent
than the coalescent time, i.e. of the order of Ne generations), and hence may not correspond to
the average recombination rate over times necessary for genomic GC-content to evolve signifi-
cantly (i.e. inter-species divergence times). Second, the precision in the estimate depends on
the physical scale at which recombination is measured. To illustrate these points let us consider
the human genome, where the impact of gBGC is well documented [6]. At the gene scale, the
correlation between present-day recombination rate (measured in a 10-kb window, centered
on the middle of the gene, using HapMap genetic map [42]), and the gene GC-content (at
third codon position) is significant but quite weak (R2 = 0.035, p<10−10). However, at 1Mb
scale the correlation is much stronger (R2 = 0.15; [9]). Furthermore, when GC-content varia-
tions and recombination rates are measured over the same evolutionary time period, the
correlation becomes very strong (1Mb scale: R2 = 0.64; [45]).
To test whether the impact of gBGC in bacteria was comparable to what is observed in
mammals, we first focused on Streptococcus pyogenes, one of the species for which the signature
of gBGC is strong (Fig. 1, see also Sup. Mat.). We computed the population-scaled recombina-
tion rate (rho) for each gene of the core genome, using ClonalOrigin [41]. The correlation be-
tween rho and the GC-content at third codon position of each gene (GC3) is higher than what
is observed in humans (R2 = 0.087; p<10−9). This result is remarkable, given that recombina-
tion rates are measured here at the gene scale (typically about 1kb).
To go further, we binned the data set into 20 groups of genes according to their GC3, and
we computed the correlation between the average GC3 and the average rho of each bin. Our
reasoning is that by computing average values, we should get estimates of rho that are more
robust to measurement noise and to possible temporal variations in recombination rates.
Using this approach, we observed a strong correlation between the GC3 and recombination
(R2 = 0.60; Fig. 3A). To investigate the amplitude of this relation in the other bacterial species
studied here, we used PREC (an index based on the proportion of genes in a bin that are detected
as recombinant by PHI), which provides a good estimate of the average recombination rate in
a bin, and is much easier to compute than ClonalOrigin’s rho. We observed a significant corre-
lation for 11 of the 14 species, and these significant correlations were positive in all cases, with
R2 values comprised between 0.24 and 0.68 (on average R2 = 0.43; Fig. 3B). Thus, in many bac-
teria, the average recombination rate in a bin is a good predictor of its average GC-content. We
performed an analogous analysis in human genes using jackknife sampling of the dataset to
scale it to the size of bacterial datasets. The average correlation observed in humans is R2 = 0.55
(Fig 3A). Hence, in many bacteria, the intensity of the relationships between GC-content and
recombination is comparable to that observed in humans, where the impact of gBGC on base
composition is known to be strong [45]. This is consistent with the hypothesis that on the long
term, the gBGC process can have a major influence on the evolution of base composition
in bacteria.

A dynamic model of the evolution of nucleotide composition: long-term

equilibrium vs. short-term disequilibrium
If the base composition of a genome is at evolutionary equilibrium then, by definition, the
number of A/T!G/C substitutions must be equal to the number of G/C!A/T substitutions.
Hildebrand and colleagues [23] noted that in a large majority of bacterial genomes (94/149),
the number of G/C!A/T changes (inferred from the comparison of closely related organisms)

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 12 / 20

 Recombination Drives the Bacterial Genome Landscape

exceeds the number of A/T!G/C changes. Given that genomic base composition strongly
fluctuates over long evolutionary times (as demonstrated by the wide distribution of GC-con-
tent across bacterial species), it is not surprising that many genomes are not at equilibrium.
However, what is unexpected is that this non-stationarity predominantly leads to loosing GC-
content: a priori, at the scale of the entire bacterial biodiversity, one would expect to observe as
many GC-increasing genomes as GC-decreasing genomes. One possible explanation is that the
observed excess G/C!A/T changes among closely related genomes corresponds to polymor-
phic mutations, which eventually do not reach fixation because either selection or gBGC favors
GC-alleles over AT-alleles [23]. Hildebrand and colleagues observed an excess of G/C!A/T
changes even in bacterial genomes that show no evidence of recent recombination population-
wise (i.e. Ner = 0) [23]. They therefore rejected the hypothesis that the fixation bias could be
due to gBGC. However, this conclusion relies on one important assumption: that the Ner
parameter measured in extant populations reflects the long-term average recombination rate.
In fact it is expected that Ne (and hence Ner) should fluctuate over time, as populations go
through periods of bottlenecks and expansion. Immediately after a bottleneck, Ner would be
close to 0, and hence genomes should accumulate G/C!A/T substitutions. However, on the
long term, this can be compensated by an increase in GC-content when the effective population
size becomes larger (and hence B > 1). Thus, the base composition of genomes may remain
above the mutational equilibrium on the long term, even if many lineages go through periods
during which Ner is null (and hence B = 0). Interestingly, the rare species for which the long-
term recombination rate is effectively null (typically endosymbiotic bacteria), generally have
very AT-rich genomes [46], as predicted by the gBGC hypothesis.

Universal mutational bias and selection on the strength of gBGC

Several lines of evidence suggest that the pattern of spontaneous mutations is biased towards
AT nucleotides, in Eukaryotes as well as Prokaryotes [22,23,47]. Under such a bias, it is ex-
pected that the selective pressure to reduce mutation rate should generally favor a GC-biased
DNA repair machinery. Recombination and repair are tightly linked processes that use many
common pathways. In yeast, the analysis of conversion tracts in meiotic product indicates that
the conversion bias is most probably due to the mismatch repair machinery (MMR) [48]. The
MMR components involved in homologous recombination (MutS, MutL) are generally con-
served between Bacteria and Eukaryotes. Hence, in Bacteria as well as Eukaryotes, gBGC could
be the secondary effect of a selection for biased repair mechanisms. However, population ge-
netics model show that when gBGC is strong, it drives the fixation of deleterious mutations
[49]. Thus, one interesting hypothesis is that in highly recombining species, selection might
favor unbiased repair mechanisms (i.e., values of b0 close to 0 in equation (1)), so as to limit the
deleterious consequences of strong gBGC. H. pylori is notorious for being highly recombining
[50,51], as confirmed by our results. It is interesting that we have found no evidence for gBGC
in this species, and recombining genes even seem to have slightly lower GC-content than non
recombining genes. This trend is however relatively weak because there is no significant trend
of variation of recombination rates among classes of homogeneous GC-content, as shown in
Fig. 3B. One possible explanation for the absence of gBGC in H. pylori could hence be that b0 is
null in this species, in compensation of a very high rate of recombination.
Although the MMR pathway is a good candidate as a molecular source of gBGC in Bacteria,
the association of gBGC with MutSL genes is not straightforward. These genes are absent from
three of our genome datasets, C. jejuni, H. pylori and Bifidobacterium longum, resulting from
ancestral losses in Delta-Proteobacteria and Actinobacteridae, respectively [52]. In H. pylori,
we indeed find no evidence of gBGC while the genomes are recombining at high frequency

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 Recombination Drives the Bacterial Genome Landscape

[50,51]. In C. jejuni and B. longum, however, we observe patterns similar to the other bacterial
datasets that are in support of the existence of gBGC, indicating that it does not depend on the
presence of a typical MutSL complex. The existence of gBGC in Bacteria and Eukaryotes
however suggests that it may have been present in the last universal common ancestor of all
cellular life forms (LUCA). Unfortunately, the only archaeal dataset matching our criteria was
a group of Sulfolobus sp. genomes for which our analysis showed few evidence of recombina-
tion (Table 1), in agreement with the previously described isolation of endemic clades in this
group [36].
We do not claim that gBGC is the unique determinant of base composition in bacterial
genome: in fact there is evidence that mutation patterns vary significantly among species [22],
and these variations are expected to contribute to differences in genome base composition.
However, the model we propose provides a simple explanation for several important results of
comparative bacterial genomics. First, gBGC can explain why bacterial genomes can maintain
a high GC-content, even though mutation is universally AT-biased [22,23]. Second, gBGC can
explain some of the intragenomic heterogeneity in GC-content observed in bacterial genomes.
Indeed, we observe that genes with evidence of recombination display on average substantially
higher GC-content than other genes. This observation also suggests that the probability of re-
combination is variable among genes in the genome, as proposed under some speciation mod-
els [53]. Furthermore, given that recently acquired genes tend to be AT-rich, gBGC would
contribute to their progressive enrichment in GC-content [54,55].

gBGC, a new component of the neutral theory of evolution

The variations of GC-content in Bacteria have long remained unexplained. The results pre-
sented here highlight a strong relationship between the GC-content of genes and their history
of recombination. This result, and the observation that bacterial genomes are generally above
the GC-content predicted from their mutational bias towards AT, are fully consistent with the
existence of gBGC. To explain our results under a selective model, one would have to hypothe-
size: i) that all bacterial species are under the same selection for higher GC throughout their
genome, ii) that this selective pressure affects all positions of a genome, independently of gene
function and expression, and iii) that the efficiency of selection varies with recombination
(Hill-Robertson interference). Incidentally, if the correlations between GC-content and recom-
bination (Fig. 3B) were due to Hill-Robertson interference, this would imply that all regions in
a genome (except possibly the most GC-rich) are mal-adapted. We favor the gBGC model be-
cause it is much more parsimonious, and it relies on mechanisms that have already been un-
covered in Eukaryotes. Ultimately, it will be possible to test experimentally the existence of
gBGC by analyzing recombination products in bacteria.
Our discovery is important because gBGC has been shown to interfere with the efficiency of
selection in Eukaryotes, and to lead to false positives in the search for regions under positive
selection in a genome. The prevalence—if not universality—of this phenomenon underlines
the importance of incorporating gBGC in the set of evolutionary forces to be considered when
searching for signature of adaption in genomes.

Materials and Methods

Genomic datasets
We used the HOGENOM database [27] to select sets of genome sequences comprising at least
six closely related strains or species. The selection of closely related genomes was based on a ge-
nomic distance derived from the HOGENOM6 database. For each pair of genomes present in
the database, we computed the best identity score, as obtained using BLAST, within each family

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 14 / 20

 Recombination Drives the Bacterial Genome Landscape

of homologous proteins as defined in HOGENOM, and averaged these scores to obtain a global
similarity score s. We then took 1-s as a distance and selected groups of genomes with at least
6 members and a distance lower than 0.15. This criterion left 21 groups of species representing
a variety of bacterial and archeal species (Table 1). For each gene family, CDSs were extracted
using ACNUC Python API [56] and re-aligned with MUSCLE [57] using default parameters.
GC% and codon frequencies were computed using custom Python scripts.

Detection of recombining genes

Detection of recombination based on multiple alignments is expected to be sensitive to both
the number of sequences aligned, and the total length of the alignment. For this reason, we
used only the universal unicopy genes of each species, and selected the 900 central positions of
each nucleotide alignment (remaining positions as well as genes shorter than this threshold
were ignored in our analysis). We used the software Phipack implementing the PHI test [28]
(parameters: window size of 100bp, p-value computed from 1,000 permutations) to test if a
gene family alignment contained evidence for recombination. Only families for which the site
permutation test could be performed were considered, i.e. where the phylogenetic signal was
sufficient to accept or reject the hypothesis of recombination. An alignment was determined to
be “recombinant” if the p-value of the permutation test was lower than 0.05. To confirm the re-
sults obtained with PHI, we also used three other tests of recombination: NSS [58], MaxChi2
[59] and Geneconv [60]. NSS and MaxChi2 statistics were computed together with PHI (as im-
plemented in Phipack package) using the same permutations to compute p-values. A consensus
of PHI, NSS and MaxChi2 was done, classifying as recombinant or non-recombinant those
gene families consistently detected by all those three methods as recombinant or non-recombi-
nant, respectively; families with disagreeing results were discarded for the consensus analysis.
Geneconv was run with the parameters “-GScale = 1 -Numsims = 10000 -Maxsimglobalpval =
0.05”, and a gene family was considered recombinant when at least one significant global re-
combinant fragment was reported; other families were considered non-recombinant. As Gene-
conv differs from the other methods on the nature of the reported evidence, it was not
considered when defining a consensus classification. Individual tests and their consensus
yielded quite different classifications of gene families, but all led to qualitatively very similar re-
sults (see S1 Fig., S3 Fig. and S4 Fig.). To test for the presence of gBGC, we performed Student’s
t-tests comparing the mean GC-content (at all or at each separate codon position) of recombi-
nant versus non-recombinant core gene family sets. All alignments as well as the results of the
various tests for recombination are available at ftp://pbil.univ-lyon1.fr/pub/datasets/DAUBIN/
Lassalle_PloS_Genet_2015

Estimation of recombination rate

We used ClonalOrigin [41] to estimate the recombination rate on full-length core gene family
alignments of 900bp or more. As ClonalOrigin inferences are highly demanding in computa-
tion time and power, we only performed this analysis on the moderately sized dataset of S.
pyogenes genomes (Spyo). The program was used with default parameter weights, running the
MCMC with 1,000,000 burn-in generations and 500,000 generations sampled every 1,000
(command line was: ‘warg -a 1,1,0.1,1,1,1,1,1,0,0,0 -x 1000000 -y 500000 -z 1000’). Families for
which this task could not be finished in less than 1 month computation were discarded, yield-
ing a total dataset of 478 gene families (out of 496 core 900bp-long ones). A number of genes
also exhibited very high variance in their estimates of rho and their exclusion yielded better
correlations with GC3.

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 15 / 20

 Recombination Drives the Bacterial Genome Landscape

Recombination inference in intergenes

Intergenic regions are evolving fast, leading to inaccurate alignments that are not amenable to
robust detection of recombination as performed on coding sequences. We thus chose to test
the relationship of intergenic GC% with recombination in a gene-centered way: for each core
protein-coding gene tested with PHI, we considered non-coding regions up to 400bp on both
sides of a CDS and averaged their GC%, provided they were of a size larger than 50bp each (to
avoid stochastic errors due to too small number of observed nucleotides). A measure of inter-
genic GC% per core gene family was obtained as the mean over all genomes of the previous
values, and was associated to the recombinant/non-recombinant status of the gene family for
further testing.

Frequencies of optimal codons

Optimal codons for each amino acid were computed by comparing synonymous codon fre-
quencies within CDSs encoding ribosomal proteins (as defined from HOGENOM family an-
notations) versus all other CDSs (RP method). Under the hypothesis of selection for highly
expressed genes to be adapted to the tRNA pool, codons statistically enriched in ribosomal
proteins (Chi-squared test based on a 2×2 contigency table of counts of occurrence at a focal
codon against those of its synonyms in ribosomal vs. other protein-coding genes, with p-value
< 0.001) were considered as “optimal”; others were classified as “non-optimal”. (S2 Table). We
then computed the absolute frequency of optimal (Fop) and non-optimal codons (Fnop) over
all coding sequences. Fop and Fnop were calculated separately for codons pooled by composi-
tion at the third position, i.e. ending in A/U or G/C. As there is a debate on whether this meth-
od is appropriate to define optimal codons [38–40], we also used an alternative definition and
took optimal codons datasets from a previous exhaustive survey of Hershberg and Petrov [38]
(HCB method). A set of optimal codons was selected when determined in Hershberg and Pet-
rov [38] study for several strains with a strong consensus, i.e. when >60% documented strains
agreed on the preferred codon and remaining strains preferred a codon with the same compo-
sition (A/U or G/C) at the third position (found in all datasets but A. baumanii) (S3 Table).

Supporting Information
S1 Text. The supplementary text contains a discussion of the various approaches available
for detecting recombination in bacteria and their pertinence for the analysis of our dataset.
(DOC)
S1 Fig. Comparison of several recombination detection programs on the inferred effect of
recombination on core genes GC-content. Legend as in Fig. 1.
(EPS)
S2 Fig. Difference of GC% between intergenes located next to recombining vs. non—
recombining genes. Difference in average GC-content of intergenic regions around each sin-
gle-copy core gene which had a conclusive result of the PHI test. Individual intergenic GC%
values were computed as the average of both flanking intergenes when they were 50bp or lon-
ger, measured on at most 400bp away of the reference gene. Intergenes were classified as re-
combinant and non-recombinant as was the neighbouring gene based on the PHI test. A
positive difference indicates that intergenes next to recombinant families are enriched in GC.
Symbols and dataset abbreviations as in Fig. 1.
(EPS)

PLOS Genetics | DOI:10.1371/journal.pgen.1004941 February 6, 2015 16 / 20

 Recombination Drives the Bacterial Genome Landscape

S3 Fig. Comparison of several recombination detection programs on the inferred effect of

recombination on codon usage of core genes, based on RP optimal codons. Legend as in
Fig. 2.
(EPS)
S4 Fig. Comparison of several recombination detection programs on the inferred effect of
recombination on codon usage of core genes, based on HCB optimal codons from
Hershberg and Petrov (2009). Legend as in Fig. 2.
(EPS)
S1 Table. Detailed results of statistical tests of difference of GC% and Fop/Fnop between re-
combining and nonrecombining core genes, varying recombination detection methods and
tested alignment length.
(XLS)
S2 Table. Sets of optimal/non-optimal codons defined using RP method.
(XLS)
S3 Table. Sets of optimal/non-optimal codons defined using HCB method. Data derived
from dataset established by Hershberg and Petrov[38].
(XLS)

Acknowledgments
We thank Gergely Szöllősi, Paul Sharp, and Eduardo PC Rocha, Nicolas Lartillot, Adam Eyre-
Walker for their thoughtful comments and advice about controls to include in the present
work. We thank Simon Penel and Vincent Miele for providing scripts and data used to process
the genomic data from HOGENOM database.

Author Contributions
Conceived and designed the experiments: FL LD VD. Performed the experiments: FL SP VD.
Analyzed the data: FL SP LD TB VD. Wrote the paper: FL TB XN LD VD.

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