High Variability of Mitochondrial Gene Order Among Fungi
High Variability of Mitochondrial Gene Order Among Fungi
High Variability of Mitochondrial Gene Order Among Fungi
Abstract
From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic
reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and
animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we
analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for
evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We inves-
tigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked
whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mt
genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition
of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of
mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may
be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated
repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.
Key words: Basidiomycota, sordariomycetes, basal fungi, fungal phylogeny, rearrangement rates, genome size reduction,
endosymbiosis.
ß The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse,
distribution, and reproduction in any medium, provided the original work is properly cited.
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 451
Aguileta et al. GBE
Kubo 2010), protists (Gray et al. 1998; Burger et al. 2003), and most ascomycetes, genes are typically encoded on the same
fungi (Paquin et al. 1997), as well as comparison among these mtDNA strand, whereas in basidiomycetes, they can be
lineages (Burger et al. 2003; Bullerwell and Gray 2004). encoded on both mtDNA strands (references in table 1).
Animal mt genomes are generally gene rich, practically Another remarkable characteristic is that, although fungi are
intron less, and they have a high rate of DNA sequence evo- a lineage more closely allied with animals, mtDNAs in these
lution. Gene order tends to be conserved, especially within organisms show signals of recombination, a characteristic that
major phyla although they can be variable between them is more similar to plant mtDNAs. Also similar to plants, fungal
(Boore 1999). In the last few years, however, examples mt genomes can have large intergenic regions including se-
from different animal groups, in particular molluscs (Boore quence repeats and introns. Interestingly, fungi have mostly
and Brown 1994; Yamazaki et al. 1997; Boore 1999; group I introns, whereas plant mitochondria tend to possess
Kurabayashi and Ueshima 2000; Rawlings et al. 2001), have preferentially group II introns (Lang et al. 2007). Intron num-
challenged this view showing that rearrangements can occur bers are highly variable in fungal mtDNA; for instance,
452 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics GBE
Table 1
List of the Species Analyzed, Accessions, and References
Species Taxonomya GenBank Accession Reference
Allomyces macrogynus Ur NC_001715 Paquin and Lang (1996)
Arthroderma obtusum E NC_012830 Wu et al. (2009)
Beauveria bassiana S NC_017842 Ghikas et al. (2010)
Candida albicans S1 NC_018046 Bartelli et al. (2013)
Candida glabrata S2 NC_004691 Koszul et al. (2003)
Chaetomium thermophilum S NC_015893 Amlacher et al. (2011)
Cordyceps bassiana S NC_013145 Ghikas et al. (2010)
Cryptococcus neoformans B NC_004336 Litter et al. (2005)
Debaryomyces hansenii S1 NC_010166 Sacerdot et al. (2008)
balance and established the context for a comprehensive anal- gene order and tRNA distribution among fungal
ysis of gene order evolution in fungi. Basal fungal taxa, being mitochondria.
highly divergent with respect to our sampled ascomycetes and
basidiomycetes, were analyzed separately to obtain reliable Materials and Methods
alignments. We investigated possible causes of gene order
variability, specifically, we assessed 1) evidence of recombina- Data Sets
tion and the dynamics of gene rearrangements and 2) the role To study the evolution of gene order in a representative data
played by intergenic regions and their associated repeats, the set of the major fungal group, the dikarya (constituted by the
number of introns, intronic ORFs, and tRNA distribution. basidiomycetes and the ascomycetes), we obtained the com-
Finally, we discuss how the combined roles of recombination, plete mt genomes and proteomes of 38 species available
chromosomal rearrangements, insertion of introns, and asso- in GenBank (table 1). The complete list of species analyzed
ciated mobile elements can contribute to the high variability of in our main data set (hereafter referred to as the
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 453
Aguileta et al. GBE
dikarya data set) includes nine basidiomycetes: Tilletia of gaps (0.1) and the consistency across aligners (>0.16)
indica (NC_010651), Phakopsora pachyrhizi (NC_014344), before they were concatenated. Subsequent phylogenetic re-
Pleurotus ostreatus (NC_009905), Cryptococcus neoformans construction combined neighbor joining and maximum likeli-
(NC_004336), Microbotryum lychnidis-dioicae (NC_020353), hood (ML), using PhyML (Guindon et al. 2009) and RAxML
Moniliophthora perniciosa (NC_005927), S. commune v.7.2.6 (Stamatakis 2006). For the ML analyses, four substitu-
(NC_003049), Trametes cingulata (NC_013933), Ustilago tion rate categories were used, estimating the gamma param-
maydis (NC_008368); 27 ascomycetes: Arthroderma obtusum eter and the fraction of invariable sites from the data. Support
(NC_012830), Beauveria bassiana (NC_017842), Cordyceps values were computed using an approximate likelihood ratio
bassiana (NC_013145), Candida albicans (NC_018046), test. Bootstrap analysis was conducted with 100 resampling
Candida glabrata (NC_004691), Chaetomium thermophilum iterations. Once we inferred the tree, we estimated evolution-
(NC_015893), Debaryomyces hansenii (NC_010166), ary rates with the r8s software v. 1.8 (Sanderson 2003). We
Dekkera bruxellensis (NC_013147), Fusarium oxysporum used the global Langley and Fitch (LF) model, which estimates
454 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics GBE
“basals,” including Al. macrogynus and Rhizophydium sp. as 1-GOC. As described in Rocha (2006), the empirical models
Neither Schizos. japonicus nor Y. lipolytica could be reliably defined in that study attempt to fit the loss of GOC with
aligned with the other clusters so they were excluded from respect to time. Model 0, proposed by Tamames (2001), is
further analysis. The complete mt genomes in each cluster the simplest model that approximates GOC to a sigmoidal
were aligned with Mauve v.2.3.1 (Darling et al. 2010) using curve described by GOC ¼ 2/1 + eat, where parameter a is
the full alignment option. This general-purpose multiple se- adjusted by regression. Model 1 fits time dependence with a
quence aligner is able to handle whole-genome alignments square root dependence, thus GOC ¼ 1 – ˇat. Model 2 con-
and has the advantage that it identifies syntenic blocks despite siders that GOC decreases with time in a negative proportion
rearrangements and reversals. We further refined the align- to the square of the GOC at time t, hence 1/GOC ¼ at + 1.
ments of the syntenic blocks using t-coffee (Notredame et al. Finally, Rocha (2006) proposes a probabilistic approach where
2000) and analyzed them with GRIMM v. 1.04 (Tesler 2002) the probability (P) of two genes staying together after t con-
and UniMoG (Hilker et al. 2012) to infer a minimal history of secutive generations is given by P ¼ pt. Thus, in Model 3:
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 455
Aguileta et al. GBE
the number of mt protein-coding genes, introns, intronic commune, and U. maydis. To our knowledge, rnpB has not
ORFs, and repeats in all our sampled genomes. We also as- been described in other basidiomycete mt genomes; it has so
sessed the distribution of tRNAs, which is variable across far only been recognized in mtDNAs of a few zygomycete and
fungal mt genomes (i.e., they can be dispersed across the ascomycete fungi, two protists, and never in animals and
genome, as in the case of Schizos. japonicus, or present in a plants (Seif et al. 2003, 2005).
few interspersed clusters, as is often the case in sordariomy- The inferred phylogenetic tree including all 38 species in the
cetes), relative to mt protein-coding genes. The number of pro- dikarya data set (fig. 1) is in agreement with previously pub-
tein-coding genes, introns, and their associated intronic ORFs, lished fungal phylogenies (Marcet-Houben and Gabaldon
as well as the number and location of tRNAs, were obtained 2009; Ebersberger et al. 2012), and most internal nodes are
from the annotations available in GenBank. Subsequently, we well supported (i.e., >90%). The global LF model that esti-
looked for simple repeats using RepeatMasker (Smit AFA, mates a single evolutionary rate across the whole tree, that is,
Hubley R, Green P. RepeatMasker Open-3.0.1996-2010; assuming a molecular clock, predicted 1.65 103 substitu-
456 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics
FIG. 1.—ML phylogeny of our sampled taxa including the 38 species in the dikarya data set. The gene tree was inferred from a concatenated alignment of 14 single-copy orthologous genes (atp6, atp8,
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
atp9, nad1–nad6, nad4L, cob, and cox1–cox3). RAxML v.7.2.6 (Stamatakis 2006) was used assuming the LG substitution matrix and default parameters. On the right side of each taxon name is a series of
colored boxes representing the mt gene order according to GenBank annotation. Bootstrap support appears next to each node. bsGOL values are shown next to each species name, and they are estimated
PP
by minimizing the following expression: L ¼ ( bi,jxj – GOLi)2, where bi,j is a Boolean variable that specifies the branches that are relevant for the estimation of a particular bsGOL (i.e., 0 if it is not relevant
and 1 if it is), xj is obtained by minimizing L and is the actual bsGOL value, and GOLi are the estimatedvalues from the pairwise comparisons, in other words, GOLi ¼ 1 GOCi (see Fischer et al. 2006 for more
details). Significant tRNA clustering was found in species marked with a spiral. This figure was made using the ETE python environment for tree exploration (Huerta-Cepas et al. 2010).
457
GBE
obtained from r8s for each clade, per fungal cluster. The
recombination events per site per time unit (Myr) were ba-
sidiomycetes (all 3 basidiomycete clusters): 0.11; sordariomy-
cetes: 0.26; saccharomycetes1: 0.02; eurotiomycetes:
0.09; dothideomycetes: 0.06; and saccharomycetes2: 0.15.
Recombination was not detected for the basal fungal cluster
with high confidence. It is noteworthy that most recombina-
tion detection programs lack power when looking for spo-
radic traces of recombination, as it is the case in mt genomes
(Posada and Crandall 2001; Barr et al. 2005; Neiman and
Taylor 2009).
Arguably, a better approach for investigating the evolution
458 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Table 2
bsGOL, NRPS Rates, and Summary of the Number of Different Genomic Elements per Species
Taxon bsGOLa Branch Lengthsb GOL Ratec Normalized GOL Rated NPRS Ratese tRNAsf Intronic ORFsg Intronsh Repeatsi Intergenic Repeatsj Genome Sizek
Cryptococcus neoformans 3.50E-01 0.7 1.05E+00 2.96E+00 0.002 20 1 2 128 9 24,874
Moniliophthora perniciosa 1.16E-01 0.22 3.36E-01 7.89E-01 0.001 30 11 13 1,648 272 109,103
Microbotryum violaceum-Sl 3.12E-01 0.25 5.62E-01 1.32E+00 0.0007 20 33 22 1,003 380 107,808
Phakopsora pachyrhizi 2.38E-01 0.7 9.38E-01 2.11E+00 0.002 24 2 5 1,898 31 31,825
Pleurotus ostreatus 1.69E-01 0.15 3.19E-01 6.38E-01 0.0009 24 9 12 645 3 73,242
Schizophyllum commune 1.39E-01 0.32 4.59E-01 9.09E-01 0.002 27 0 0 1,718 61 49,704
Tilletia indica 8.97E-02 0.2 2.90E-01 5.74E-01 0.0008 24 0 0 568 52 65,147
Fungal Mitochondrial Genomics
Trametes cingulata 3.00E-01 0.16 4.60E-01 9.11E-01 0.0006 25 26 26 1,196 143 91,500
Ustilago maydis 1.71E-01 0.14 3.11E-01 6.16E-01 0.0005 23 11 12 337 37 56,814
Candida albicans 2.37E-01 0.24 4.77E-01 1.22E+00 0.003 30 0 2 279 40 40,420
Debaryomyces hansenii 1.64E-01 0.19 3.54E-01 8.64E-01 0.004 25 4 4 389 20 29,462
Dekkera bruxellensis 2.15E-01 0.26 4.75E-01 1.16E+00 0.003 25 3 5 3,968 939 76,453
Millerozyma farinosa 2.16E-01 0.2 4.16E-01 9.83E-01 0.004 25 11 14 710 31 39,107
Ogataea angusta 1.41E-01 0.4 5.41E-01 1.54E+00 0.004 26 6 6 944 46 41,719
Pichia pastoris 1.29E-01 0.21 3.39E-01 8.76E-01 0.002 25 3 6 1,080 21 35,683
Mycosphaerella graminicola 1.97E-01 0.16 3.57E-01 8.43E-01 0.0007 27 0 0 218 66 43,964
Peltigera malacea 9.28E-02 0.2 2.93E-01 8.35E-01 0.001 26 17 20 468 31 62,785
Phaeosphaeria nodorum 2.03E-01 0.18 3.83E-01 1.09E+00 0.0009 27 2 4 667 36 49,761
Arthroderma obtusum 7.66E-02 0.02 9.66E-02 2.48E-01 0.0007 25 1 1 325 14 24,105
Microsporum canis 7.66E-02 0.02 9.66E-02 2.38E-01 0.0007 25 1 1 344 10 23,943
Paracoccidioides brasiliensis 1.54E-01 0.24 3.94E-01 9.26E-01 0.001 25 3 13 552 175 71,335
Penicillium marneffei 2.38E-01 0.16 3.98E-01 9.19E-01 0.0007 28 9 11 303 16 35,438
Beauveria bassiana 2.90E-02 0.002 3.10E-02 7.38E-02 0.0002 25 5 5 284 10 29,961
Chaetomium thermophilum 1.45E-01 0.1 2.45E-01 6.29E-01 0.0008 28 3 3 927 113 127,206
Cordyceps bassiana 5.53E-02 0.009 6.43E-02 1.65E-01 0.0005 24 4 5 295 10 32,263
Fusarium oxysporum 5.37E-02 0.01 6.37E-02 1.66E-01 0.0006 25 1 2 298 1 34,477
Gibberella zeae 5.67E-02 0.02 7.67E-02 2.00E-01 0.0006 28 33 35 529 48 95,676
Lecanicillium muscarium 8.50E-02 0.05 1.35E-01 3.54E-01 0.002 25 1 1 241 9 24,499
Metarhizium anisopliae 1.46E-01 0.12 2.66E-01 6.97E-01 0.001 24 1 1 220 2 24,673
Podospora anserina 2.01E-01 0.09 2.91E-01 6.87E-01 0.0008 27 31 34 326 48 100,314
Allomyces macrogynus 1.97E-01 0.3 4.97E-01 7.44E-01 0.0004 25 10 28 219 14 57,473
Rhizophydium sp.136 3.65E-01 1.2 1.56E+00 3.84E+00 0.002 7 1 1 809 13 68,834
Schizosaccharomyces japonicus 5.08E-01 0.87 1.38E+00 3.38E+00 0.002 25 3 2 928 94 80,059
Yarrowia lipolytica 2.00E-01 0.56 7.60E-01 1.76E+00 0.002 27 15 17 792 72 47,916
Candida glabrata 9.56E-02 0.09 1.86E-01 2.78E-01 0.001 23 3 3 797 68 20,063
Kluyveromyces lactis 3.49E-01 0.14 4.89E-01 1.09E+00 0.001 22 3 3 1,190 279 40,291
Nakaseomyces bacillisporus 8.18E-02 0.2 2.82E-01 7.33E-01 0.003 23 0 0 7,896 3,791 107,123
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Vanderwaltozyma polyspora 2.62E-01 0.17 4.32E-01 1.06E+00 0.002 23 0 0 1,258 186 21,684
a PP
bsGOL values were estimated by minimizing the following expression: L ¼ ( bi,jxj – GOLi)2, where bi,j is a Boolean variable that specifies the branches that are relevant for the estimation of a particular bsGOL (i.e., 0 if it
is not relevant and 1 if it is), xj is obtained by minimizing L and is the actual bsGOL value, and GOLi are the estimated values from the pairwise comparisons, in other words, GOLi ¼ 1 GOCi (see Fischer et al. [2006] for more
details).
b
These branch lengths were obtained by ML phylogenetic reconstruction with RaxML (Stamatakis 2006).
c
bsGOL normalized by the branch length.
d
bsGOL rates normalized relative to the mean GOL rate value.
e
Rates obtained with r8s with the nonparametric method minimizing local transformations (NPRS) and optimization via Powell’s method (Sanderson 2003).
f
Number of tRNAs (GenBank).
g
Number of intronic ORFs (GenBank).
h
Number of introns (GenBank).
i
Number of repeats (whole genome) detected with Repeatmasker (Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0.1996-2010; http://www.repeatmasker.org, last accessed February 18, 2014).
j
Number of intergenic repeats detected with mreps (Kolpakov et al. 2003).
459
GBE
k
Genome size in bp (GenBank).
Table 3
Number of Intergenic Repeats Normalized by the Number of Species
in Each Fungal Cluster, with and without Outliers, and Rearrangement
Events per Fungal Cluster
Fungal Cluster Intergenic Intergenic Rearrangement
Repeats Repeats Events
(without
Outliers)a
Basidiomycetes 988 (109.78) 336 (37.33) 414
Sordariomycetes 241 (30.13) 32 (4) 42
Dothideomycetes 133 (44.33) 133 (44.33) 24
Eurotiomycetes 215 (53.75) 40 (10) 22
Saccharomycetes1 1,097 (182.83) 158 (26.33) 156
460 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics GBE
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 461
Aguileta et al. GBE
Among the genomic elements studied here, repeats at sequences are not divergent enough for software to detect
intergenic regions show the strongest correlation with gene them (at least two phylogenetically informative sites must exist
order. According to theoretical studies, the accumulation of to each side of the recombination breakpoint [Martin et al.
repeats, among other mtDNA structural features, seems to be 2011]). Also, the power to detect recombination depends on
driven mostly by drift and mutation pressure, which are in turn the effective population size, which in the case of mitochon-
largely determined by population size dynamics (e.g., genome dria depends on the bottleneck levels attributable to mt trans-
size reduction or bottlenecks (Lynch and Blanchard 1998; mission (Neiman and Taylor 2009). Finally, although in
Lynch et al. 2006). Although intron-associated ORFs, in par- principle there is one homologous site per base available for
ticular those encoding HEs, have a great potential to insert homologous recombination, there are many more sites avail-
copies in different locations within the genome, thereby able for nonhomologous recombination. This is consistent
changing gene order, we did not observe a strong correlation with the latter type of recombination being more likely to
with gene rearrangements. If they play a role in shaping gene promote gene order changes.
462 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics GBE
reports (Gordenin et al. 1993; Bi and Liu 1996; Lobachev et al. Bi X, Liu LF. 1996. DNA rearrangement mediated by inverted repeats. Proc
1998; Rocha et al. 1999; Waldman et al. 1999; Rocha 2003, Natl Acad Sci U S A. 93:819–823.
Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:
2006; Phadnis et al. 2005; Odahara et al. 2009; Lavrov 2010). 1767–1780.
Transposable elements and variability of tRNA distribution also Boore JL, Brown WM. 1994. Complete DNA-sequence of the mitochon-
appear to contribute to gene order variability although appar- drial genome of the black chiton, Katharina tunicata. Genetics 138:
ently less strongly. 423–443.
Bouchier C, Ma L, Creno S, Dujon B, Fairhead C. 2009. Complete mito-
chondrial genome sequences of three Nakaseomyces species reveal
Supplementary Material invasion by palindromic GC clusters and considerable size expansion.
FEMS Yeast Res. 9:1283–1292.
Supplementary figures S1–S3 and tables S1–S5 are available Bruen TC, Philippe H, Bryant D. 2006. A simple and robust statistical
at Genome Biology and Evolution online (http://www.gbe. test for detecting the presence of recombination. Genetics 172:
oxfordjournals.org/). 2665–2681.
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 463
Aguileta et al. GBE
Gabaldon T, Huynen MA. 2003. Reconstruction of the proto-mitochon- in mtDNAs of sordariomycetes: phylogenetic implications. Fungal
drial metabolism. Science 301:609–609. Genet Biol. 41:930–940.
Gabaldon T, Huynen MA. 2004. Shaping the mitochondrial proteome. Kueberl A, et al. 2011. High-quality genome sequence of Pichia pastoris
Biochim Biophys Acta. 1659:212–220. CBS7435. J Biotechnol. 154:312–320.
Gabaldon T, Huynen MA. 2007. From endosymbiont to host-controlled Kurabayashi A, Ueshima R. 2000. Complete sequence of the mitochon-
organelle: the hijacking of mitochondrial protein synthesis and metab- drial DNA of the primitive opisthobranch gastropod Pupa strigosa:
olism. PLoS Comput Biol. 3:2209–2218. systematic implication of the genome organization. Mol Biol Evol.
Gabaldon T, Rainey D, Huynen MA. 2005. Tracing the evolution of a large 17:266–277.
protein complex in the eukaryotes, NADH: ubiquinone oxidoreductase Lambowitz AM, Perlman PS. 1990. Involvement of aminoacyl-transfer
(complex I). J Mol Biol. 348:857–870. RNA-synthetases and other proteins in group-I and group-II intron-
Galtier N. 2011. The intriguing evolutionary dynamics of plant mitochon- splicing. Trends Biochem Sci. 15:440–444.
drial DNA. BMC Biol. 9:61. Lang BF, Laforest M-J, Burger G. 2007. Mitochondrial introns: a critical
Ghikas DV, Kouvelis VN, Typas MA. 2006. The complete mitochondrial view. Trends Genet. 23:119–125.
genome of the entomopathogenic fungus Metarhizium anisopliae var. Lavrov DV. 2010. Rapid proliferation of repetitive palindromic elements in
464 Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014
Fungal Mitochondrial Genomics GBE
Pantou MP, Kouvelis VN, Typas MA. 2008. The complete mitochondrial Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylo-
genome of Fusarium oxysporum: insights into fungal mitochondrial genetic analyses with thousands of taxa and mixed models.
evolution. Gene 419:7–15. Bioinformatics 22:2688–2690.
Paquin B, Lang BF. 1996. The mitochondrial DNA of Allomyces macrogy- Stone CL, Posada Buitrago ML, Boore JL, Frederick RD. 2010. Analysis of
nus: the complete genomic sequence from an ancestral fungus. J Mol the complete mitochondrial genome sequences of the soybean rust
Biol. 255:688–701. pathogens Phakopsora pachyrhizi and P. meibomiae. Mycologia 102:
Paquin B, et al. 1997. The fungal mitochondrial genome project: evolution 887–897.
of fungal mitochondrial genomes and their gene expression. Curr Tamames J. 2001. Evolution of gene order conservation in prokaryotes.
Genet. 31:380–395. Genome Biol. 2:RESEARCH0020.
Pellenz S, Harington A, Dujon B, Wolf K, Schafer B. 2002. Characterization Taylor JW, Berbee ML. 2006. Dating divergences in the fungal tree of life:
of the I-SpomI endonuclease from fission yeast: insights into the evo- review and new analyses. Mycologia 98:838–849.
lution of a group I intron-encoded homing endonuclease. J Mol Evol. Tesler G. 2002. GRIMM: genome rearrangements web server.
55:302–313. Bioinformatics 18:492–493.
Perseke M, et al. 2008. Evolution of mitochondrial gene orders in echino- Torriani SFF, Goodwin SB, Kema GHJ, Pangilinan JL, McDonald BA. 2008.
Genome Biol. Evol. 6(2):451–465. doi:10.1093/gbe/evu028 Advance Access publication February 6, 2014 465