Mitochondrial Genome Evolution in a Single
Protoploid Yeast Species
Paul P. Jung,1Anne Friedrich,1Cyrielle Reisser, Jing Hou, and Joseph Schacherer2
Department of Genetics, Genomics and Microbiology, University of Strasbourg/Centre National de la Recherche
Scientifique, Unité Mixte de Recherche 7156, Strasbourg, France
ABSTRACT Mitochondria are organelles, which play a key role in some essential functions, including
respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial
DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to
elucidate the structural diversity of these genomes. Although a large corpus of data are now available on
the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To
study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide
polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We
determined the complete mt genome sequences of strains isolated from various geographical locations (in
North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of
the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea
thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast
species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri
provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although
these genomes are completely syntenic, their size and the intron content were found to vary among the
isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and
6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level
of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection
in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These
data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.
The mitochondrion is a central organelle, which participates in key
cellular functions such as respiration, metabolite biosynthesis, ion
homeostasis, and apoptosis. These essential cellular processes are
conserved in all eukaryotic organisms, from humans to yeasts.
However, the mitochondrial DNA (mtDNA) has been found to show
a greater rate of mutation than the nuclear DNA. The mtDNA
mutation rate and spectrum have been determined by performing
mutation-accumulation experiments on a wide range of model organ-
isms, including Caenorhabidtis elegans (Denver et al. 2000), Caeno-
rhabidtis briggsae (Howe et al. 2010), Pristionchus pacificus (Molnar
et al. 2011), Drosophila melanogaster (Haag-Liautard et al. 2008), and
Saccharomyces cerevisiae (Lynch et al. 2008). The mutation rates are
high (around of 1028to 1027per site per generation) in all these
species, but they vary from one species to another.
Studies on yeasts, especially those belonging to the Hemiascomy-
cetes phylum, have contributed considerably to our understanding of
interspecific mitochondrial (mt) genome evolution. Complete mito-
chondrial genome sequences are now available on more than 40
hemiascomycetous species covering a broad evolutionary range
(Solieri 2010; Gaillardin et al. 2011). The availability of these genome
sequences provided an opportunity for us to investigate the changes in
the patterns of mtDNA organization and genome architecture from
the evolutionary perspective. The size of mt genomes varies between
yeast species, ranging, for example, from 11 to 85 kb in Hanseniaspora
uvarum and S. cerevisiae, respectively (Foury et al. 1998; Pramateftaki
Copyright © 2012 Jung et al.
Manuscript received May 22, 2012; accepted for publication July 9, 2012
This is an open-access article distributed under the terms of the Creative
Commons Attribution Unported License (http://creativecommons.org/licenses/
by/3.0/), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
Supporting information is available online at http://www.g3journal.org/lookup/
1These authors contributed equally to this work.
2Corresponding author: University of Strasbourg/CNRS, 28 rue Goethe, Strasbourg,
67083 France. E-mail: firstname.lastname@example.org
Volume 2|September 2012|
et al. 2006). Despite this high level of diversity, a core set of genes is
conserved. This core contains the genes encoding the apocytochrome
b (COB), three subunits of ATP synthetase (ATP6, ATP8, and ATP9)
and three subunits of cytochrome oxidase (COX1, COX2, and COX3).
In addition, mtDNAs encode both large (LSU) and small (SSU) rRNA
genes and a complete set of tRNA genes. However, some variability of
the gene content is also observed among yeasts. Several genes, includ-
ing those encoding VAR1 (a ribosomal protein), RPM1 (the RNA
subunit of the mitochondrial RNaseP), and the seven NADH:ubiqui-
none oxidoreductase (complex I) subunits do not occur consistently in
all yeast mt genomes. The fact that the gene order varies significantly
indicates that a large number of rearrangements has occurred with
time (Bouchier et al. 2009; Jung et al. 2009, 2010; Valach et al. 2011).
A few exceptions have been observed, however, where the synteny is
conserved across species. The gene order is completely conserved
between Candida parapsilosis, Candida orthopsilosis, and Candida
metapsilosis, which are closely related species as well as between spe-
cies of the Yarrowia clade, which are phylogenetically more distantly
related species (Kosa et al. 2006; Gaillardin et al. 2011).
The many complete yeast mt genome sequences published by now
have shown the existence of considerable variations and a wide range
of genome architectures among species. Despite the existence of this
ever-increasing body of data, relatively little is known so far about the
mitochondrial genome variations existing within single yeast species.
Due to the lack of intraspecific mitochondrial data, the evolution of
mtDNA has not yet been completely elucidated. Because the differ-
ences between the mt genomes of various wild yeast isolates have not
so far been documented, it was proposed here to investigate the
patterns of mtDNA diversity present in a single yeast species by
conducting a comprehensive survey on a set of Lachancea kluyveri
(formerly known as Saccharomyces kluyveri) yeast isolates. L. kluyveri
strains can be isolated from various sources such as soil, Drosophila,
and tree exudates. Unlike S. cerevisiae, this species has not been
domesticated (Liti et al. 2009; Schacherer et al. 2009). In addition,
L. kluyveri is a protoploid Saccharomycetaceae, which means that it
diverged from the S. cerevisiae lineage before undergoing ancestral
whole-genome duplication (WGD) and is therefore a pre-WGD yeast
species (Souciet et al. 2009). Interestingly, in species belonging to the
Saccharomyces genus that underwent WGD, the nuclear genes acting
in the mitochondria show a greater rate of evolution than the other
genes, which suggests that the mitochondrial functions have weakened
in these post-WGD yeasts (Jiang et al. 2008). These findings can be
correlated with the fact that most post-WGD species can live without
a functional mt genome with their ability to generate petite mutants
(Merico et al. 2007). Unlike the Saccharomyces species, L. kluyveri is
petite-negative and mainly ferments sugar in the absence of oxygen
(Piskur et al. 1998; Møller et al. 2001). We therefore expected
L. kluyveri to be a suitable model organism for studying intraspecific
yeast mt genome evolution.
Here, we present the complete mt genome sequences of 18
L. kluyveri strains, which were isolated from various geographical
locations (in North America, Asia, and Europe) and ecological niches
(Drosophila, tree exudates, and soil). We first assembled the mt ge-
nome of the NCYC 543 reference strain (also known as CBS 3082),
the nuclear genome of which was recently sequenced (Souciet et al.
2009). This genome is 51,525 bp long and contains the same set of 35
genes as those described in Lachancea thermotolerans (CBS 6340
strain), its closest relative (Talla et al. 2005). To provide a better
picture of the genetic diversity among L. kluyveri species, we com-
pared the mtDNA of these 18 isolates. This species is composed of two
geographically defined lineages corresponding to the North American
and European isolates. The genomes are syntenic, but the size of the
mtDNA and the intron content differ. Whole-mtDNA genome anal-
ysis clearly showed the presence of a greater rate of SNPs and indels
in the intergenic regions than in the coding regions. The dN/dS ratios
obtained clearly suggested that purifying selection purged most non-
synonymous differences from the protein-coding genes. Only the dN/
dS ratio obtained in the case of the VAR1 gene was exceptionally high,
possibly due to changes in the functional constraints to which this
gene was exposed.
MATERIAL AND METHODS
Strains and DNA preparation
Strains to be sequenced were selected so as to maximize the range of
sources and the types of location from which they were isolated. The
list of the 18 L. kluyveri strains used in this study, which were pur-
chased from various yeast culture collections, is given in supporting
information, Table S1.
Yeast cell cultures were grown overnight at 30? in 20 mL of YPD
medium up to the early stationary phase. Total genomic DNAs were
subsequently extracted using the QIAGEN Genomic-tip 100/G in line
with the manufacturer’s instructions.
Sequencing and assembly
Genomic paired-end Illumina sequencing libraries were prepared with
a mean insert size of 280 nt. The 18 libraries were multiplexed in 2
Illumina HiSeq2000 lanes for sequencing. Paired-end reads from 102
nt, six of which were dedicated to the multiplex tag, were obtained,
amounting to 149,308,900 paired-end reads in all. FASTX-Toolkit
(http://hannonlab.cshl.edu/fastx_toolkit/) was first used with options
“-t 20 -l 50” to clean the reads. Two independent de novo assemblies
(ace63 and ace75) were then constructed with each strain using
SOAPdenovo, version 1.05 (Li et al. 2010), with two different Kmer
sizes (soapdenovo63mer with option –K 63 and soapdenovo127mer
with –K 75).
Mitochondrial reference sequence construction
The assemblies obtained with strain NCYC 543 were used to construct
a mitochondrial reference sequence corresponding to the L. kluyveri
species. We identified mitochondrial contigs and scaffolds within
ace63 and ace75 assemblies by performing similarity searches with
the BLAST suite of programs (Altschul et al. 1997) using L. thermo-
tolerans mitochondrial gene sequences as the query (Talla et al. 2005).
A total number of 135 scaffolds and contigs were highlighted in these
two independent assemblies, among which 98 were redundant. The 37
remaining sequences were compared with MUMmer 3.0 (Kurtz et al.
2004) to detect overlapping segments and the alignment of all these
sequences was refined manually to obtain a single contig.
The protein-coding genes as well as the large and small subunits of
the ribosomal RNA genes were exactly located on the complete
mitochondrial sequence by performing BLASTN searches with
L. thermotolerans genes. The COX1 and COB intronic regions were
refined manually based on the conservation of the protein sequences.
The position of introns within the LSU genes was determined based
on the boundaries defined for both S. cerevisiae and L. thermotolerans
species (Jacquier and Dujon 1983).
The same procedure was used to assemble and annotate the
complete mitochondrial sequences of the 55-86.1, 77-1003, CBS 6547,
and CBS 5828 strains for intraspecific comparison purposes. We
|P. P. Jung et al.
obtained complete mitochondrial contigs for the 55-86.1 and 77-1003
strains. By contrast, there are one gap of 49 bp and two gaps of 30 and
40 bp in the scaffold of CBS 5828 and CBS 6547, respectively.
HE664110 for the NCYC 543 strain, HE774680 for the 55-86.1 strain,
HE664111 for the 77-1003 strain, HE774664 for the CBS 6547 strain,
and HE664112 for the CBS 5828 strain.
The coding sequences of ATP6, ATP8, ATP9, COB, COX1, COX2,
COX3, and VAR1 genes were extracted from the initial ace63 assembly
of the L. kluyveri strains by performing similarity searches with NCYC
543 gene sequences as the query. The sequences of all the genes were
recovered in all strains except for the CBS 10368 strain, in which
VAR1 could not be completed. The VAR1 gene was therefore removed
from the phylogenetic analysis. The nucleotide sequences of these
genes were automatically aligned with MUSCLE (Edgar 2004) and
manually inspected before being concatenated.
Based on these 5475 aligned positions, phylogenetic relationships
among L. kluyveri strains were analyzed using neighbor-joining (using
the Kimura two-parameter substitution model), maximum likelihood
(using the Hasegawa-Kishino-Yano 85 substitution model), and
Bayesian (10,000 generations, sampling trees every 10 generations,
discarding the first 250 trees as a burn-in) methods. These analyses
were performed with SeaView (Gouy et al. 2010), PhyML (Guindon
and Gascuel 2003), and MrBayes (Dereeper et al. 2008), respectively.
Bootstrap analyses (1000 replications) were used to assess the confi-
dence level of each node for the Neighbor-joining method.
Selection and dN/dS ratios
The dN/dS ratios were calculated using CODEML model in PAML
package version 4.4b (Yang 2007). We used a tree-based maximum-
likelihood method. To summarize, coding sequence multi-alignments
was generated for each of the eight protein-coding genes among the
set of 18 L. kluyveri, as described previously. Based on the alignments,
neighbor-joining trees were constructed using ClustalX and then la-
beled manually considering the branch-length and genetic proximity
of the strains. Estimates of the dN/dS ratios were then calculated for
The estimation of the number of population clusters was performed
with the Structure program, version 2.3.1 (Pritchard et al. 2000), based
on the 180 polymorphic positions detected in the seven protein-coding
sequences previously used for the phylogenetic analyses. We ran the
Structure program using the admixture model with the population
number parameter K set from two to four, on 100,000 replicates after
a burn-in of 100,000 iterations and did not incorporate any prior
population information in these analyses.
To investigate the intraspecific mtDNA variations present in yeast, we
sequenced complete mitochondrial genomes from a set of 18 L. kluy-
veri isolates. These strains were isolated in various countries world-
wide from ecological sources of various kinds (insect guts, tree
exudates, and soil; Table S1). The complete mt genome sequences
were determined directly using high-throughput sequencing methods.
Illumina libraries were constructed from genomic DNA isolated from
the various strains and run on two lanes of a flow cell on an Illumina
HiSeq 2000 using 102-bp paired-end sequencing methods. In this way,
a coverage of 100% was obtained and the average read depth was
Mitochondrial genome of L. kluyveri
The nuclear genome of the reference NCYC 543 strain (also known as
CBS 3082) was previously sequenced, but the mt genome was not
sequenced (Souciet et al. 2009). This strain was isolated from the
intestinal canal of Drosophila pinicola in the Yosemite National Park
of California in the United States. We first assembled the mt genome.
When we used SOAPdenovo, assembly of the reads yielded a single
scaffold, which is 51,525 bp long and shows a GC content of about
15% (Table S2). This mitochondrial sequence is more than twice the
size of that obtained in the closely related species L. thermotolerans
[CBS 6340 strain (Talla et al. 2005)]. Despite this difference in size, the
same set of 35 genes is encoded by the two genomes, both being
transcribed from only one DNA strand (Figure 1). Among these 35
genes, eight are protein-coding genes and 27 are noncoding RNA
genes. The protein-coding genes encode three subunits of the cyto-
chrome c oxidase (COX1, COX2, and COX3), three subunits of the
ATP synthase (ATP6, ATP8, and ATP9), the apocytochrome b (COB)
and a ribosomal protein (VAR1). The noncoding RNA genes comprise
two genes encoding the small and large RNA subunits of the ribosome
(SSU and LSU, respectively), the RPM1 gene that codes for the RNA
subunit of the RNaseP and 24 tRNA genes. The RPM1 gene was
detected using three conserved regions among ascomycete fungi,
named CRI, CRIV, and CRV (Seif et al. 2003). This gene is located
between tRNAProand tRNAMet: this location is the same as that pre-
viously found to occur in S. cerevisiae and L. thermotolerans (Foury
et al. 1998; Talla et al. 2005). The set of tRNA genes includes at least
one tRNA for each of the 20 amino acids and sufficed to be able to
decipher the fungal mitochondrial genetic code. This genetic code
differs from standard code because mtDNA encodes a tRNATrpable
to decode UGA codon as it has been reported for several yeast species
including L. thermotolerans (Talla et al. 2005).
Complete analysis of gene conservation order between the mt
genomes of L. kluyveri and L. thermotolerans showed that these two
sequences are almost completely syntenic (Figure 1). With the ex-
ception of the two tRNAs surrounding the COX2 gene, these two
genomes are colinear, which suggests that a very low rate of gross
chromosomal rearrangements of mtDNA has occurred in the
Lachancea clade (Figure 1). Despite the high levels of synteny ob-
served, comparisons between entire mt genomes of L. kluyveri and
L. thermotolerans showed the existence of considerable genomic
variability, especially in the noncoding sequences. This variability
explains the size differences observed, for example. The twofold size
difference is found to be correlated with the relative size of the
intergenic regions, which ranges from 22.3% in L. thermotolerans
to 41% in L. kluyveri (Table S2), as well as with the difference
between the intron content of three genes: COB, COX1, and LSU.
Unlike the L. thermotolerans COB gene, which is intronless, that of
L. kluyveri harbors two introns. In addition, although the COX1
genes of those two species both contain three introns, the third
one is almost two times larger in L. kluyveri than in L. thermotoler-
ans (Figure 1). All the introns present in the protein-coding genes of
L. kluyveri, apart from the first intron in the COB gene, encode
endonucleases belonging to the LAGLIDADG family of group I
introns (Haugen et al. 2005). An intron was also detected in the
LSU gene, with the same downstream boundary as that described in
S. cerevisiae and an upstream boundary containing only one addi-
tional nucleotide (Jacquier and Dujon 1983).
Volume 2September 2012|Yeast Mitochondrial Genome Evolution|
Intraspecific diversity in the mitochondrial
To explore the intraspecific variability, DNA sequence diversity in the
coding region was first compared among 18 L. kluyveri isolates. A
total number of 208 polymorphic positions (3.16% of the sites on the
6591 bp) showed a nucleotide substitution. The frequency of polymor-
phism is 0.0098 per bp on average. Among the 1101 SNPs identified
in coding genes, 171 are nonsynonymous and 930 are synonymous
(Table S3). This imbalance strongly suggests that purifying selection
has purged the nonsynonymous differences from the protein-coding
To determine the effects of purifying selection, we then quantified
the selective constraints present in the mt genomes by estimating the
ratio of nonsynonymous (dN) to synonymous (dS) substitution rates
v = dN/dS. We calculated the average v ratio in each of the coding
genes (Figure 2). In all the cases studied, dN was lower than dS,
signature of strong purifying selection of mitochondrial genes (Figure
S1). Median values of v lower than 1 were obtained in all the genes,
but the values differed from one gene to another (Figure 2). The
ATP8, ATP9, and COX3 gene ratios were lower than average. In
addition, the ATP6 and VAR1 genes were found to be characterized
by a dN/dS ratio, which is well above average, giving a median value of
0.21 and 0.35, respectively. This finding might potentially be attribut-
able either to positive selection or to a reduced constraint level on
these genes. The results observed for VAR1 gene is interesting not only
because of the elevated dN/dS ratio but also because we observed an
exceptionally low dS value (the lowest in this set) and high dN value
than average (the second highest in this set) (Figure S1).
Intraspecific diversity of the intron content
The mitochondrial intron content is known to vary among closely
related yeast species (Jung et al. 2010; Gaillardin et al. 2011). The
results obtained here show that this is also the case between members
of the same species (Table S2). All the introns present in protein-
coding genes belong to the group I intron family and encode an
endonuclease, with the exception of the first intron in the COB gene.
In the various L. kluyveri mt genomes studied, it is worth noting that
the intron content is highly variable in the COB and COX1 genes
(Figure S2). The intron patterns seem to depend on the geographical
origin of the strains. All the strains originating from North America
contain the same two introns in the COB gene, whereas the number of
introns ranges from two to four in the Eurasian strains (Figure S2). The
first intron detected in the North American strains (between amino
acids 132 and 133) occurs in 9 of the 11 Eurasian strains, whereas the
second one (between amino acids 168 and 169) occurs in all the latter
strains. A supplementary intron was found to exist between amino
acids 143 and 144 in five of the seven European strains and two of
the four Asian strains. The Asian strains also contain a specific intron
located between amino acids 237 and 238, which suggests that the
pattern of evolution differed. The difference in the intron content is
even more pronounced in the case of the COX1 gene. The Eurasian
isolates contain four to five introns, in different combinations depend-
ing on the strains. All the Asian strains contain a first intron composed
of two LAGLIDADG motifs and lack the last intron occurring in the
European strains, with the exception of CBS 10367. The intron pattern
of the European strains seems to be well conserved in comparison with
the Asian strains, which suggests that the latter strains may have
evolved independently from European ones. More surprisingly, the
North American strains (62-196, CBS 6545, and CBS 6547) contain
an additional intron located between amino acids 300 and 301.
All in all, these data clearly show that the intron content varied
considerably between the isolates studied. This high rate of in-
traspecific intron variation suggests that the intron dynamics may
contribute crucially to the structure of mitochondrial genomes.
Figure 1 Overview of the organization of the mtDNA of L. kluyveri. The mtDNA of L. thermotolerans is also shown so as to be able to compare
the structure and the synteny. Protein-coding genes and tRNA and rRNA genes are presented in dark blue, red, and green, respectively. Coding
introns are represented in light blue and noncoding introns in white. The RPM1 gene is presented in yellow.
Figure 2 Box-plot comparisons of the dN/dS ratio [v] estimated in the
various mt genes and based on pairwise alignments.
| P. P. Jung et al.
Phylogeny of the L. kluyveri species
To shed light on the intraspecific mitochondrial evolution in L. kluy-
veri and compare the effects of geographical vs. ecological origins on
strain diversity, we investigated the phylogenetic relationships among
the strains surveyed. A phylogenic tree was built based on the con-
catenation of the aligned ATP6-ATP8-ATP9-COX1-COX2-COX3-
COB coding sequences. A standard neighbor-joining method was used
to build a majority-rule consensus tree based on the 18 mt genomes
under investigation (Figure 3). The phylogenetic tree clearly shows the
existence of two tight clusters, which diverge from each other. We
deduced that these two clusters consist of isolates of different geo-
graphical origins. The clades corresponding to these two clusters con-
tain either the North American samples (clade 1) or the Eurasian
samples (clade 2; Figure 3). High bootstrap values support the exis-
tence of the node between the two clusters. A similar topology was
observed using two other methods (Bayesian and maximum likeli-
hood methods) to build the tree (Figure S3). This phylogeny strongly
supports the hypothesis that the evolution of the L. kluyveri species
depended on their geographical location. By contrast, the ecological
environment does not seem to have been a key factor in the evolution
of L. kluyveri, as several strains recovered from tree exudates were
found to be present in both clades.
In addition, single gene phylogenies based on the coding sequences
of the two largest genes (COB and COX1) as well as the evolution of
the intron pattern suggest that clade 2 could be subdivided into sub-
clades, the first of which corresponded to the Asian strains and the
second to the European ones (Figure S4). These differences probably
emerged more recently than that observed between clades 1 and 2.
Population structure provides clear-cut evidence
for geographical isolation
Phylogenetic trees do not show the true evolutionary history of strains,
since they mask the effects of outcrossing among strains (Ruderfer
et al. 2006). The population structure was therefore inferred here from
the polymorphic sites across mitochondrial sequences. We used the
model-based clustering algorithm implemented in the program Struc-
ture (Pritchard et al. 2000). This analysis largely confirmed the results
of the phylogenetic analysis (Figure 4). The results obtained with this
program were consistent with the existence of two main populations
forming major geographical subgroups. The North American and
Eurasian strains belong to two distinct well-defined populations (Fig-
ure 4). Some SNPs represent private polymorphism within each pop-
ulation, resulting in a clear-cut separation between these two
populations. The CBS 6547 strain is the only one that can be said
to be a mixture of two populations when the K parameter (i.e. the
number of predicted populations) was equal to two.
However, the increase in the K parameter shows that our collection
contained two clean populations. One of them is composed of four
North American strains (55-86.1, 77-1003, NCYC 543, and 62-1041),
whereas the second one consists of four European strains (dd281a,
CBS 2861, CBS 4568, and DBVPG 3108; Figure 4). The existence of
these two populations is consistent with the phylogenetic distribution
Figure 3 Neighbor-joining tree
of 18 L. kluyveri strains. The tree
was constructed based on the
concatenation of mt genes, corre-
sponding to 5475 polymorphic
positions. Numbers are bootstrap
values based on 1000 replicates.
Volume 2September 2012| Yeast Mitochondrial Genome Evolution|
previously observed, as bootstrap values of 100 were associated with
both ancestral nodes. By contrast, the other 10 strains are part of
mixed-populations, as they seem to be mostly composed of a combi-
nation of 2 populations. The genomes of the other three North Amer-
ican strains (CBS 6545, 62-196, and CBS 6547) as well as those of all
the Asian strains are mosaics showing a mixed architecture. The
present structural analysis clearly shows that the Asian isolates studied
here are not members of a clear population. These results show that
the L. kluyveri species is structured and composed of two clean line-
ages, corresponding to the North American and European popula-
tions (Figure 4).
Whole mitochondrial genome comparisons
As suggested previously, the reason why the protein coding genes are
well conserved is that purifying selection has eliminated many
mutations. To investigate the mitochondrial genome-wide pattern of
mitochondrial polymorphism, we compared the reference genome
(NCYC 543) with four other mt genomes. Three of them belong to
clade 1 (55-86.1, 77-1003, and CBS 6547) and one (CBS 5828) to clade
2 (Figure 3). Assembly of the reads yielded a single scaffold for each
mt genome. As was to be expected, it turned out that exactly the same
set of 35 genes is encoded by these mitochondrial genomes and that
the synteny is perfectly conserved. The absence of rearrangements of
the mtDNA in the L. kluyveri species is not surprising, in a view of the
fact that practically no genomic rearrangements exist between L. kluy-
veri and L. thermotolerans.
However, differences in size were observed between these mt
sequences (Table S2): they range from 50,137 bp in the case of CBS
6547 to 53,726 bp in that of CBS 5828. This difference can be partly
explained by the difference in the intron contents mentioned previ-
ously. The North American sequences were found to have the same
intron content, whereas CBS 5828 harbors three additional introns. In
addition, a decrease in the size of the intergenic region was observed
between the distal strains, from 41% in the case of 772103 to 28% in
that of CBS 5828 (Table S2). This difference is mainly due to the
variability of the region located between the ATP9 and COX2 genes,
which decreases in size from almost 3 kb in the case of 7721003 to
700 bp in that of CBS 5828.
Figure 4 Population structure
of the 18 L. kluyveri strains.
Cluster results from a structure
analysis on 180 polymorphic
sites. Each strain is represented
by a single vertical bar, which is
partitioned into K-colored seg-
ments that represent the strain’s
estimated ancestry proportion
in each of the K clusters.
|P. P. Jung et al.
We also analyzed the genome-wide pattern of polymorphism
(Table 1). The great diversity observed in the intergenic regions con-
trasts with the existence of highly conserved coding regions. In the
coding region, the SNP density ranges from 0 to 13.96 SNPs/kb in
55286.1 and CBS 5828, respectively. By contrast, the SNP density is
much greater in the intergenic regions, where it ranges from 0.31 to
82.7 SNPs/kb in the same genomes. We also detected a total number
of 1196 insertion and deletion events (indels). Single-base indels are
the most common size class, and about half of them are less than five
bases long in size (Figure S5). A few large deletions (up to 1695 bases
in size) were detected in the CBS 6547 and CBS 5828 genomes. These
strains are genetically more distantly related to the NCYC 543 refer-
ence strain than the others. Interestingly, a very large number of indels
were detected in the intergenic regions. Among the 1196 indels ob-
served, 1123 (93.9%) occur in intergenic regions, which account for
only 57% of the genome on average, and only five occur in coding
regions. These data suggest once again that most of the indels present
in protein-coding genes were removed by selection. In addition, the
density of the indels (0.19 indels/kb on average) is much lower than
that of the SNPs (5.19 SNPs/kb on average) in the coding genes. This
paucity of indels probably reflects the fact that most of the indels have
resulted in frameshifts, and thus to a nonfunctional protein. By con-
trast, intergenic regions, which are mostly selectively neutral regions,
show a very high density of SNPs (37.2 SNPs/kb on average) as well as
indels (9.8 indels/kb on average). All in all, these data strongly suggest
that most of the mutational events affecting the protein sequence have
been purged by selection.
The availability of mt genomes from single isolates of various
hemiascomycetous yeast species has improved our understanding of
mtDNA evolution at different levels (Eldarov et al. 2011; Jung et al.
2010; Kosa et al. 2006; Pramateftaki et al. 2006; Prochazka et al. 2010).
Comparative genomic studies on these genomes have shown the ex-
istence of many differences in their structure, organization, and to-
pology (Solieri 2010). However, no comparisons have been carried out
so far on single yeast species. Some whole-mtDNA genome studies re-
cently shed interesting light on selection and evolution in humans (Batini
et al. 2011; Elson et al. 2004; Gunnarsdóttir et al. 2011, Schönberg et al.
2011). To investigate the genetic diversity and the patterns of mitochon-
drial genome evolution occurring in a single yeast species, we sequenced
the complete mtDNA of 18 L. kluyveri isolates. In addition, the data we
generated will help us to have a better understanding of phenotypic
variation linked mtDNA diversity.
One aim of this study was to assess the evolutionary history of the
L. kluyveri species. Mitochondrial coding sequences of the 18 isolates
were used to investigate the phylogeny by various methods. All the
phylogenetic analyses clearly showed that the genomes sequenced
comprised two tight clusters, corresponding to the North American
and Eurasian isolates (Figure 3). To investigate the evolutionary his-
tory of these strains more closely, the population structure was also
determined and the data obtained yielded some useful information
about the populations in question (Figure 4). They also suggested that
the genetic variations observed in L. kluyveri have a geographical basis.
Evolutionary patterns based on geographical origin have previously
been described, especially in the S. paradoxus species (Liti et al. 2009).
Studies on the variability of this species clearly showed the existence of
four populations originating from Europe, the Far East, America, and
Hawaii (Liti et al. 2009). The evolution of S. cerevisiae strains was
found on the contrary to be highly correlated with the ecological
niches from which they originated rather than with their geographical
origins (Schacherer et al. 2009). A clear-cut population structure was
observed in the main ecological subgroups. These populations result
from separate domestication events, but S. cerevisiae as a whole is not
a domesticated species (Liti et al. 2009).
All these data give an overall picture of the intraspecific variability
of the yeast mt genome. In terms of their size and intron content, the
yeast mt genomes of this species are highly variable (Table S2). The
size ranged from 50.1 to 53.7 kb in CBS 6547 and CBS 5828, re-
spectively. These differences may be attributable to either the intron
content or the length of the intergenic regions. In fact, there exists
a balance between the variations in these two regions. The size of
intergenic regions varies between 15 to 21.2 kb, whereas the intron
content varies both in number (between 6 and 9) and size (between
8.7 kb and 12.8 kb; Table S2). The large genome size of the CBS 5828
isolate can be explained, for example, by the presence of nine introns,
amounting to 12.8 kb. All the coding introns identified in the various
yeast genomes studied here belong to the group I introns and encode
endonucleases. It was established long time ago that group I introns
are mobile elements, which can be gained or lost (Delahodde et al.
1989; Dujon et al. 1989; Wenzlau et al. 1989). The patterns of intron
content observed in the wild isolates are interesting because they
indicate that the mt genomes show a high level of intraspecific plas-
ticity (Figure S2). These patterns are correlated with the phylogeny of
the strains and are therefore similar between strains originating from
similar geographical locations. In addition to the difference in size and
intron content, the gene content and order are conserved across the
strains, as suggested by previous interspecific genome comparisons.
Whole-mtDNA genome studies also provide a good means of
addressing selection issues. These issues have been extensively studied
in humans (Batini et al. 2011; Gunnarsdóttir et al. 2011; Schönberg
et al. 2011). To investigate the patterns of polymorphism involved in
mitochondrial genome evolution among L. kluyveri isolates, we quan-
tified the selective constraints to which each of the mitochondrial
genes was exposed by estimating v. These ratios were found to be
very low and consistent among the genes studied, with the noteworthy
exception of the VAR1 gene, which gave a very high ratio. The low
dN/dS ratios of most of the other mitochondrial genes provide evi-
dence for purifying selection, i.e., most of the amino acid substitutions
which occurred were deleterious and were therefore removed. Despite
n Table 1 Polymorphic patterns in mitochondrial genomes of 4 L. kluyveri isolates
Pairwise Comparison With NCYC 543 as Reference
Coding RegionsIntergenic Regions
SNP, single-nucleotide polymorphism.
Volume 2 September 2012|Yeast Mitochondrial Genome Evolution|
this purifying selection, we found definite evidence for relaxed puri-
fying selection for two genes. First, the ATP6 gene is characterized by
a greater than average v value (median value, 0.21). The ATP6 gene is
one of three mitochondrial genes, the others being ATP8 and ATP9,
which encode ATP synthase subunits. The most interesting point
here, however, is the particularly high v value obtained in the case
of the VAR1 gene (median value: 0.35). The VAR1 gene encodes
a mitochondrial ribosomal protein of the small subunit. Interestingly,
VAR1 is not found in all the yeast mitochondrial genomes, and shows
a scattered pattern of distribution among hemiascomycetous yeasts
(Jung et al. 2009). The most parsimonious explanation for the relax-
ation of the purifying selection should be a reduced functional con-
straint in the VAR1 gene.
Genome-wide patterns of SNPs and indels were also studied.
Large disparities were noted between the distribution of the poly-
morphisms observed in the coding and intergenic regions (Table 1).
The mean density of nucleotide polymorphism was estimated at 5.2
SNPs/kb in the coding region and 37.2 SNPs/kb in the intergenic
regions. This high figure is also consistent with the effects of puri-
fying selection. This selection was also reflected in the high indel
density in the intergenic regions (9.8 indels/kb on average), whereas
they amounted to only 0.19 indels/kb on average in the coding
regions. These data suggest once again that most of the indels in
protein-coding genes were removed by selection. In addition, it is
worth noting that most of the indels were found to be single-base or
very small indels (Figure S5). The fact that indels are mostly con-
centrated in homopolymers also suggests that sequence variations
may have been caused by replication slippage events (Behura 2007,
Noutsos et al. 2005).
The overall density of nucleotide polymorphism of the mt ge-
nomes studied here is very high, amounting 28.5 SNPs/kb on average,
which is 10-fold greater than that previously observed in the nuclear
genome of S. cerevisiae (2.8 SNPs/kb on average) (Schacherer et al.
2009). This finding seems to confirm that the mtDNA shows a higher
mutation rate than the nuclear genome (Clark-Walker 1991; Lynch
and Blanchard 1998; Lynch et al. 2006; Lynch 2007). In S. cerevisiae,
mutation-accumulation lines have been used to estimate the rate of
nucleotide substitution in nuclear and mt genomes (Lynch et al.
2008). Nucleotide substitution rates have been estimated to be 37-fold
greater in the mitochondria than in the nuclei. There are several
explanations for this high mutation rate. First, mtDNA undergoes more
replication and may accumulate more mutations than nuclear DNA
explaining the hypermutability state of the organelle. In S. cerevisiae, the
mtDNA genome is present normally at 202100 copies per cell com-
prising 10–20% of the total cellular DNA (Williamson and Fennell
1979). Second, there is a low efficient of the DNA repair pathway (Song
et al. 2005). Finally, the intracellular environment is more mutagenic
The intraspecific diversity of the yeast mt genome was described
here in detail for the first time. As mentioned previously, the content
and order of the genes have been completely conserved. By contrast,
the size, intron content and the intergenic regions were found to vary
from one isolates to another. The pattern of variation observed among
the mitochondrial genes, with the exception of the ATP6 and VAR1
genes, is consistent with purifying selection. It would now be inter-
esting to determine the rates and patterns of mtDNA in close relatives
of this species such as Lachancea cidri, Lachancea fermentati, Lachan-
cea meyersii, and Lachanceawaltii(Naumovaetal. 2007).Such a study
could address the issues of selection and compare the patterns of mt
sequence variation at two hierarchical levels: within species and
among closely related species.
We thank Michael Knop for kindly providing us with the dd281
L. kluyveri strain. We are most grateful to Vladimir Benes from the
Gene Core Facilities EMBL (Heidelberg, Germany). We sincerely
thank Bernard Dujon for helpful discussions and critical reading of
the manuscript. This work was supported by an ANR grant (2010-
BLAN-1606-05). C.R. is supported by a grant from CNRS and Région
Alsace. J.S. is supported by an ANR grant (2011-JSV6-004-01).
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Inference of population
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Communicating editor: A. Rokas
Volume 2 September 2012|Yeast Mitochondrial Genome Evolution|