Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex.
ABSTRACT The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human pathogens. Although R. oryzae reportedly has a heterothallic (+/-) mating system, most strains have not been observed to undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina, Zygomycota). In all of these fungi, the minus (-) allele features the SexM high mobility group (HMG) gene flanked by an RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes, including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species. When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores, while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.
- SourceAvailable from: Peter Edward Mortimer[Show abstract] [Hide abstract]
ABSTRACT: Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.Fungal diversity 01/2014; · 6.94 Impact Factor
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ABSTRACT: Tuber spp. are filamentous ascomycetes which establish symbiosis with the roots of trees and shrub species. By virtue of this symbiosis they produce hypogeous ascocarps, known as truffles. Filamentous ascomycetes can reproduce by homothallism or heterothallism depending on the structure and organization of their mating type locus. The first mating type locus in a truffle species has been recently characterized in Tuber melanosporum and it has been shown that this fungus, endemic in Europe, is heterothallic. The availability of sequence information for T. melanosporum mating type genes is seminal to cloning their orthologs from other Tuber species and assessing their reproductive mode. Here we report on the organization of the mating type region in T. indicum, the black truffle species present in Asia, which is the closest relative to T. melanosporum and is characterized by an high level of morphological and genetic variability. The present study shows that T. indicum is also heterothallic. Examination of Asiatic black truffles belonging to different genetic classes, sorted according to the sequence polymorphism of the internal transcribed spacer rDNA region, has revealed sequence variations and rearrangements in both coding and non-coding regions of the mating type locus, to suggest the existence of cryptic species within the T. indicum complex. The presence of transposable elements within or linked to the mating type region suggests a role of these elements in generating the genotypic diversity present among T. indicum strains. Overall, comparative analyses of the mating type locus have thus allowed us to tackle taxonomical and phylogenetic issues within black truffles and make inferences about the evolution of T. melanosporum-T. indicum lineage. Our results are not only of fundamental but also of applied relevance as T. indicum produces edible fruit bodies that are imported also into Europe and thus may represent a biological threat for T. melanosporum.PLoS ONE 12/2013; 8(12):e82353. · 3.53 Impact Factor
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ABSTRACT: The fungal kingdom displays a fascinating diversity of sex-determination systems. Recent advances in genomics provide insights into the molecular mechanisms of sex, mating type determination, and evolution of sexual reproduction in many fungal species in both ancient and modern phylogenetic lineages. All major fungal groups have evolved sexual differentiation and recombination pathways. However, sexuality is unknown in arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota, an ecologically vital group of obligate plant root symbionts. AMF are commonly considered an ancient asexual lineage dating back to the Ordovician, approximately 460 M years ago. In this study, we used genomic and transcriptomic surveys of several AMF species to demonstrate the presence of conserved putative sex pheromone-sensing mitogen-activated protein (MAP) kinases, comparable to those described in Ascomycota and Basidiomycota. We also find genes for high mobility group (HMG) transcription factors, homologous to SexM and SexP genes in the Mucorales. The SexM genes show a remarkable sequence diversity among multiple copies in the genome, while only a single SexP sequence was detected in some isolates of Rhizophagus irregularis. In the Mucorales and Microsporidia, the sexM gene is flanked by genes for a triosephosphate transporter (TPT) and a RNA helicase, but we find no evidence for synteny in the vicinity of the Sex locus in AMF. Nonetheless, our results, together with previous observations on meiotic machinery, suggest that AMF could undergo a complete sexual reproduction cycle.PLoS ONE 11/2013; 8(11):e80729. · 3.53 Impact Factor
Structure, Function, and Phylogeny of the Mating Locus
in the Rhizopus oryzae Complex
Andrii P. Gryganskyi1,2*, Soo Chan Lee3, Anastasia P. Litvintseva3, Matthew E. Smith1, Gregory Bonito1,
Teresita M. Porter1, Iryna M. Anishchenko2, Joseph Heitman3, Rytas Vilgalys1
1Department of Biology, Duke University, Durham, North Carolina, United States of America, 2Department of Mycology, M.G. Kholodny Institute of Botany, National
Academy of Sciences of Ukraine, Kyiv, Ukraine, 3Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United
States of America
The Rhizopus oryzae species complex is a group of zygomycete fungi that are common, cosmopolitan saprotrophs. Some
strains are used beneficially for production of Asian fermented foods but they can also act as opportunistic human
pathogens. Although R. oryzae reportedly has a heterothallic (+/2) mating system, most strains have not been observed to
undergo sexual reproduction and the genetic structure of its mating locus has not been characterized. Here we report on
the mating behavior and genetic structure of the mating locus for 54 isolates of the R. oryzae complex. All 54 strains have a
mating locus similar in overall organization to Phycomyces blakesleeanus and Mucor circinelloides (Mucoromycotina,
Zygomycota). In all of these fungi, the minus (2) allele features the SexM high mobility group (HMG) gene flanked by an
RNA helicase gene and a TP transporter gene (TPT). Within the R. oryzae complex, the plus (+) mating allele includes an
inserted region that codes for a BTB/POZ domain gene and the SexP HMG gene. Phylogenetic analyses of multiple genes,
including the mating loci (HMG, TPT, RNA helicase), ITS1-5.8S-ITS2 rDNA, RPB2, and LDH genes, identified two distinct
groups of strains. These correspond to previously described sibling species R. oryzae sensu stricto and R. delemar. Within
each species, discordant gene phylogenies among multiple loci suggest an outcrossing population structure. The
hypothesis of random-mating is also supported by a 50:50 ratio of plus and minus mating types in both cryptic species.
When crossed with tester strains of the opposite mating type, most isolates of R. delemar failed to produce zygospores,
while isolates of R. oryzae produced sterile zygospores. In spite of the reluctance of most strains to mate in vitro, the
conserved sex locus structure and evidence for outcrossing suggest that a normal sexual cycle occurs in both species.
Citation: Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, Bonito G, et al. (2010) Structure, Function, and Phylogeny of the Mating Locus in the Rhizopus oryzae
Complex. PLoS ONE 5(12): e15273. doi:10.1371/journal.pone.0015273
Editor: Darren P. Martin, Institute of Infectious Disease and Molecular Medicine, South Africa
Received July 28, 2010; Accepted November 4, 2010; Published December 9, 2010
Copyright: ? 2010 Gryganskyi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported in part by National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases R01 grant AI50113 to J. H.
and R21 grant AI085331 to J. H. S. C. L. was supported by the NIH Molecular Mycology and Pathogenesis Training Program (AI52080). The funders had no role in
study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: firstname.lastname@example.org
Rhizopus oryzae is a complex of closely related, heterothallic
species [1,2,3,4] that are common, cosmopolitan saprotrophs in
soil, dung, and rotting vegetation [5,6,7,8]. Strains of the R. oryzae
complex have been used for centuries as fermented food starters
[9,10,11,12,13,14] but species in this group can also act as
opportunistic, invasive animal and human pathogens that cause
deadly infections in immuno-compromised individuals [15,16,17,
Like other fungi belonging to subphylum Mucoromycotina,
members of the R. oryzae complex have a bipolar mating system
[21,22]. Compatible (+) and (2) mating types are recognizable by
their mating behavior and subsequent production of meiospores
(zygospores). However, mating behavior is not always consistent
among different strains. Furthermore, zygospore germination and
progeny development within the genus Rhizopus appears to be rare
and has only been documented in a few cases [19,21].
The mating behavior of Rhizopus species represents a distinct
pattern of zygospore production among Mucoralean fungi known
as the ‘‘Rhizopus pattern’’. In this type of zygospore formation,
some nuclei fuse while others degenerate and meiosis is delayed
until zygospore germination [21,23]. Zygospores have been
observed in both heterothallic and homothallic Rhizopus species
[3,4] but in most cases they do not germinate. Although zygospore
germination is rare, it has been documented for R. stolonifer
[24,25,26]. In addition, some Rhizopus species produce azygos-
pores, which are thought to be asexual. They are morphologically
similar to zygospores but develop in the absence of a mating
Recent studies of sexual reproduction in the zygomycete
Phycomyces blakesleeanus revealed that the mating system of this
species is regulated by divergent alleles of a single gene: SexM (2)
and SexP (+) . The sex gene is a member of the high mobility
genes (HMG) family and is located between two flanking genes
that code for a triose-phosphate transporter homolog (TPT) and
an RNA helicase . A similar sex locus structure was also
reported in another zygomycete, Mucor circinelloides  and was
predicted for R. oryzae based on BLAST analysis of the publicly
available genome of strain RA99-880 . A recent study also
found a similar sex-related locus in three Microsporidian species,
PLoS ONE | www.plosone.org1December 2010 | Volume 5 | Issue 12 | e15273
which are believed to be closely related to the zygomycetes
In this study, we characterized the sex locus in six strains of the
R. oryzae species complex (four (2) strains and two (+) strains) and
examined the genetic structure of the sex locus in a larger collection
of clinical, industrial, and environmental isolates. We identified the
most conserved regions in the sex locus and designed primers for
three key regions: the high mobility group (HMG) gene regions,
the triose-phosphate transporter (TPT) region, and the RNA
helicase region. We used these primers to amplify fragments of the
sex locus from 40 additional isolates and used these DNA
sequences to study phylogenetic relationships among loci. Here
we compare the phylogenetic pattern from the sex genes with those
from several other commonly sequenced DNA loci (ITS1-5.8S-
ITS2 and 28S rDNA, RPB2, mtSSU) and demonstrate that the sex
loci are informative for differentiating the cryptic sibling species R.
oryzae s. s. and R. delemar. We also compare the sex locus structure of
R. oryzae (+) and (2) strains with those of the two mucoralean fungi
Phycomyces blakesleeanus and Mucor circinelloides and show that the sex
locus of all three taxa has a similar overall arrangement.
Mating tests produce sexual spores but not progeny
We repeated the mating tests reported by Schipper  using the
same strains: (+) CBS346.36 and (2) CBS110.17, CBS112.07
CBS264.28, CBS266.30, CBS329.47, and CBS382.52. We were
not able to include the holotype culture of Rhizopus delemar
(CBS120.12, GenBank # AB181318), but we have included the R.
delemar strain NRRL21447, which has an ITS1-5.8S-ITS2
sequence that is identical to that of the type culture (Fig. S1A).
As observed by Schipper, zygospores formed in all mating
reactions except those performed with (2) strain CBS257.28.
We also tested additional R. oryzae isolates from the NRRL and
Duke collections using the tester strains CBS346.36 (+) and
CBS112.07 (2). These mating tests identified six additional
compatible isolates that were capable of producing zygospores
when paired with tester strains of the opposite mating type
(Table 1, Table S3). Self-pairings or pairings with senescent
cultures consistently failed to produce zygospores. Mating test
results were not influenced by medium type, medium nutrient
concentration, or Petri plate size. Most strains did not produce
zygospores with either ‘‘plus’’ or ‘‘minus’’ testers under the
conditions we tested. The genome strain RA99-880 also failed to
produce zygospores in all mating tests with any of the 55 strains
used in this study.
Where mating occurred, zygospores developed within two to
three weeks. Although complete darkness is required for successful
mating tests of some zygomycetes (e. g. Mucor spp.) , we
determined that R. oryzae group isolates formed zygospores in
partial light or in complete darkness. During mating, most
zygomycetes form a straight line of zygospores at the interface
between the two compatible strains, which has been reported
previously for R. oryzae  (C. Skory, personal communication).
However, we did not observe the typical straight line of zygospores
and instead found them diffusely distributed across the plate within
ca 4 to 5 cm of the inoculation points. The majority of the
zygospores were observed on the side of the Petri plate where the
(+) strain was growing.
Under the light microscope, initiation of individual zygospores
between two conjugating hyphae could be observed. Conjugating
hyphae were consistently shorter and thicker than vegetative
hyphae, and were separated from vegetative hyphae by visible
Table 1. Isolates of the Rhizopus oryzae complex used in this
Collection # Zygospores
type Origin and notes
R. oryzae s. s.
CBS112.073, 4, 5
CBS148.22 yes minus1, 2
as R. tonkinensis, lactic acid
as R. formosaensis, fermented
CBS266.30 yesminus1, 2
as R. fusiformis, on Brassica root
CBS382.52 yesminus1, 2
Duke99-133 non. d. human pathogen
NRRL1897 yesminus1, 2
NRRL2908 yesplus1, 2
parsnip, produces steroids
soft red wheat
NRRL21789 yes plus2
NRRLA-336yes minus1, 2
NRRLA-13440 yesminus1, 2
CBS329.47 yesminus1, 2
tempeh, produces pectinase
produces fumaric acid
1determined in mating assays.
2determined by sequencing the sex locus.
3Strains for which the sex locus and flanking genes have been sequenced.
5Tester strains used in mating assays.
n. d. – not determined.
Mating Locus in Rhizopus oryzae
PLoS ONE | www.plosone.org 2December 2010 | Volume 5 | Issue 12 | e15273
septae. After zygospore formation, conjugating hyphae developed
into asymmetric suspensor cells (Fig. 1) . Zygospores were
morphologically variable and ranged from 60–140 mm in
diameter. Zygospore shape ranged from round to flat with stellate
conical projections (Fig. S2A) and color ranged from reddish
brown to dark brown. As in previous mating studies of R. oryzae s.
l., we also observed large, central vacuoles inside many zygospores
Contrary to published results for R. stolonifer [25,26], we were
unable to stimulate germination of zygospores into germospor-
angia under any of the experimental conditions tested. Gentle
crushing of exospore (outer zygospore wall)  resulted in the
release of protoplast material, which developed into a vegetative
mycelium (Fig. S2C). Fourteen single spore isolates were
germinated and grown in 100 ml of PD medium overnight.
DNA was extracted from these cultures as previously described for
standard isolates. Using the described primers, we obtained DNA
sequences for the sex locus of these isolates and determined that all
14 single spore isolates had only the (2) mating type.
Structure of the mating locus in R. oryzae
Recent studies demonstrated that P. blakesleeanus and M.
circinelloides have similar sex genes [16,27]. The sex locus and the
flanking genes in both species consists of a 7–10 kb region that
includes a gene encoding a high mobility protein (HMG) that is
flanked by a gene encoding a TP transporter (TPT) and a second
gene coding for an RNA helicase. DNA sequences of P.
blakesleeanus and M. circinelloides were used to screen the publicly
available genome of R. oryzae and identify the sex locus in R. oryzae
. The sex locus of R. oryzae is located in a 13 kb region in
Supercontig 1 (R. oryzae database, http://www.broadinstitute.org/
annotation/genome/rhizopus_oryzae/MultiHome.html). It en-
codes proteins with 48% and 58% total amino acid identity with
the (+) sex loci of P. blakesleeanus and M. circinelloides, respectively.
Unlike P. blakesleeanus and M. circinelloides, which have sex and TPT
genes in an inverted orientation [16,27], the sex and flanking genes
of both (+) and (2) strains of R. oryzae are oriented in the same
direction (Fig. 2).
We designed specific PCR primers to amplify the sex locus from
five representative strains of R. oryzae; one of which contained the
putative (+) mating type and four strains with the putative (2)
mating type. DNA sequencing confirmed that the mating locus
structure of R. oryzae is similar to those of P. blakesleeanus and M.
circinelloides and consists of an HMG gene (SexP/SexM) flanked by
TP transporter and RNA helicase genes (Table 2, Fig. 2). The
mating genes (HMG, TPT, and RNA helicase) of the (+) strains of
these three species share 24% amino acid identity (49% similarity
at the DNA level). The (2) alleles of these three species share 30%
amino acid identity (92% similarity at the DNA level).
The RNA helicase gene is 4161–4191 bp long and includes nine
introns of 40–150 bp each. This gene was annotated in the R.
oryzae database as transcript RO3G_01291 in Supercontig 1. The
TP transporter gene, which is not yet annotated in the R. oryzae
database, is 1336 bp long and belongs to the EamA-like
transporter family. We also identified the putative protein-coding
gene  with an ORF that was located between the TPT gene
and the HMG gene in both the (+) genome strain RA99-880 and
the (+) tester strain CBS346.36. Parts of this gene are annotated in
the R. oryzae database as transcripts RO3G_01290 (1482 bp),
RO3G_01289 (1831 bp), and RO3G_01288 (625 bp). These
transcripts were identified as an Ankyrin repeat region, a BTB/
POZ region, and a third protein of unknown function,
respectively. This three-part region BTB/Ankyrin/RCC1 (Fig. 2)
 is absent in all of the (2) strains that we tested as well as the
publicly available genomes of Phycomyces blakesleeanus and Mucor
circinelloides [16,27]. The presence of BTB/Ankyrin/RCC1
accounts for the fact that the sex locus and flanking gene
complexes from (2) strains are smaller (7 kb) than in the (+)
strains (13.3 kb). Aside from BTB/Ankyrin/RCC1, the structure
and direction of the flanking genes is similar in (2) and (+) strains.
Strain RA99-880, used to obtain the genome sequence of R.
oryzae , did not mate with any of the isolates that we tested.
This observation led us to question whether this isolate represents
R. oryzae or a different Rhizopus species (Table 3). We compared the
(+) mating alleles of RA99-880 to CBS346.36. We previously
determined that CBS346.36 produced zygospores when mated
with the holotype culture of R. oryzae CBS112.07, suggesting that
they are likely conspecific. We determined that the HMG box
region in the (+) strain CBS346.36 was 942 bp long, contained no
introns, and shared only 93% DNA sequence identity with
genome strain RA99-880.
In addition, we compared the structures of the HMG box
region between (2) and (+) alleles. The (2) allele encodes a protein
that is 180 amino acids in length whereas the (+) allele encodes a
protein that is 253 amino acids in length. Both (+) and (2) alleles
share 23% nucleotide identity but both contain an identical amino
acid motif at the 59-end of their sequences: RP(T)NAF(I)LY. This
motif is nearly identical to the motifs found in both the (+) and (2)
strains of Phycomyces blakesleeanus and Mucor circinelloides.
Figure 1. Zygospores of Rhizopus oryzae. A cross between
CBS346.36 (+) and CBS110.17 (2) was analyzed with light microscopy
(A) and scanning electron microscopy (B). Zygospores (white arrow
heads) are attached to an asymmetric suspensor (black arrow heads).
Scale=20 mm. Asterisks indicate conjugated hyphae during early stage
of zygospore formation.
Mating Locus in Rhizopus oryzae
PLoS ONE | www.plosone.org3 December 2010 | Volume 5 | Issue 12 | e15273
Multilocus phylogenetic studies
Comparative analysis of mating loci between two (+) and four
(2) strains of R. oryzae revealed that two (+) strains, CBS346.36 and
RA99-880, shared 93.3% amino acid identity. Although the DNA
sequences from (2) strains were more conserved, we still detected
significant differences between isolates: these four strains shared
98.4–100% amino acid identity. This genetic divergence between
isolates of the same mating type prompted analysis of genetic
diversity among multiple isolates of R. oryzae.
To determine genetic relationships among isolates, we obtained
partial sequences of the HMG gene from 57 strains using PCR
primers specific for (+) and (2) mating alleles. Based on their DNA
sequences, 26 strains belonged to the (+) type and 29 strains
belonged to the (2) type (Table S3). These partial sequences were
used for determining phylogenetic relationships among the strains.
Eleven haplotypes of the (+) HMG locus were identified, which
were separated into two distinct groups on the ML tree (Fig. 3A).
Fifteen different haplotypes of the (2) HMG locus were identified,
which also were separated into two well-supported phylogenetic
groups (Fig. 3B). We also obtained partial sequences from the two
flanking genes, TPT and RNA helicase. Eighteen TPT and 16
RNA helicase haplotypes were detected among the 41 strains.
Gene trees for each locus strongly support two clades (Figs. S1C,
D). Four additional gene regions commonly used in fungal
systematics (mitochondrial small-subunit RNA (mtSSU), nuclear-
encoded large subunit RNA (nLSU 28S), ITS1-5.8S-ITS2 region
and RPB2) were also sequenced from the complete set of 57
clinical and environmental strains (Table S3). MtSSU and rDNA
28S genes were too highly conserved to provide phylogenetic
resolution within the R. oryzae complex (data not shown). In
contrast, phylogenetic analysis of the more variable rDNA ITS1-
5.8S-ITS2 and RPB2 regions revealed the same two well-
supported clades detected by the analysis of the mating loci.
Phylogenetic analysis of the concatenated data set containing all
four loci (rDNA ITS1-5.8S-ITS2, RPB2, TPT and RNA helicase)
also strongly supports two major clades (Fig. 3C, also Fig. S1A).
These two clades correspond to two cryptic species, Rhizopus oryzae
sensu stricto and R. delemar, that had been previously recognized
based on LDH genes and ITS sequencing .
Although separate and combined gene trees all support
evidence for two cryptic species, phylogenetic relationships among
strains within each species varied depending on which gene was
used. This is also illustrated by the failure of consensus trees to
resolve phylogenetic relationships within either cryptic species
(Fig. 3D). A phylogenetic congruence test  revealed significant
discordance among gene phylogenies attributable to within-species
recombination among all 4 loci (partition homogeneity test,
p=0.001). This scenario, whereby multiple gene trees consistently
resolve the phylogeny between but not within species, is the basis
for the Phylogenetic Concordance Species Concept advocated by
Taylor et al. .
When we mapped results of the mating experiments to the
ITS+RPB2+TPT+RNA helicase phylogeny (Fig. 3C) we deter-
mined that many isolates of R. oryzae s. s. were capable of
producing zygospores when paired with isolates of the opposite
mating type. Specifically, three (+) and eight (2) strains out of 33
R. oryzae s. s. isolates (11/33 or 33%) were capable of a successful
mating reaction as defined by the production of zygospores. In
contrast, most R. delemar strains were sterile. Only three of 21 R.
delemar strains were capable of producing zygospores when paired
Figure 2. Comparison of sex locus structure in the Mucorales
(Mucoromycotina, Zygomycota). (A) Dot plot showing the diver-
gent DNA sequence of sexP and sexM genes in Rhizopus oryzae, whereas
the TPT and RNA helicase genes are highly conserved. The orientations
of sexP and sexM genes are the same in R. oryzae. (B) sex locus structures
of P. blakesleeanus and M. circinelloides  are compared with R. oryzae
(this study). Relative to R. oryzae, the TPT gene in M. circinelloides and
both the TPT gene and sexP in P. blakesleeanus have an inverted
orientation. The (+) allele of R. oryzae contains an additional gene
between the TPT gene and sexP that is not found in the other two
species or in the (2) allele of R. oryzae. Black boxes show repetitive
sequence tracts, arrows show gene orientation, and lines represent
Mating Locus in Rhizopus oryzae
PLoS ONE | www.plosone.org4 December 2010 | Volume 5 | Issue 12 | e15273
with the (+) tester strain CBS346.36 (3/21 or 14%). However,
none of the strains produced zygospores when paired with the (+)
genome strain RA99-880 from the same clade.
Distribution of mating types within each cryptic species
To test if the distribution of the two mating types was the same
in populations of R. oryzae and R. delemar, we used mating gene-
specific PCR primers to assign mating types to 57 different strains.
All strains possessed either a (+) or a (2) HMG mating allele
(mating allele type could not be determined for two strains). As
expected, (+) strains were only capable of mating with (2) strains
and vice versa. In each species, the ratio of plus/minus mating types
is close to 1:1, evidence that is consistent with a randomly mating
population. Within R. oryzae, the ratio of +/2 isolates was
observed to be 14:18 (chi-square with one degree freedom =0.5,
two tailed p=0.4795). For R. delemar this ratio of plus/minus was
12:11 (chi-square=0.043, p=0.8348). For all isolates combined
(regardless of species) this ratio (26:29) is also not significantly
different from 50:50 (chi-square=0.164, p=0.6568).
Asexual sporangiospores of R. oryzae and R. delemar are
When grown on agar media, all R. oryzae complex strains have
similar growth patterns and growth rates. Actively growing
colonies fill a 90 mm Petri dish in 2 to 3 days at room temperature
(23uC). After 3 to 4 days, most isolates begin to produce
sporangiospores (Fig. S2B), although some strains sporulate more
slowly and may require 10 to 14 days.
In an effort to delimit R. oryzae from R. delemar isolates based on
morphology, we measured the length and width of sporangio-
spores from 20 randomly chosen strains. The R. oryzae and R.
delemar isolates we studied showed no observable differences in
spore size (Fig. 4). Size differs considerably even for the spores
produced by the same sporangium (Fig. 5), which reflects the
different number of nuclei per spore. Binucleate sporangiospores
are considerably larger than uninucleate ones (Fig. S2D). Our
findings agree with previous studies  that both R. oryzae and R.
delemar can have a wide and overlapping range of spore sizes. The
length to width ratio remains approximately constant at 1.3.
Spore surface area was strain-specific for each of 12 randomly
selected R. oryzae complex isolates (Fig. S3). However, we were
unable to determine a specific pattern distinguishing sporangio-
spores of R. oryzae from R. delemar.
Rhizopus oryzae s. s. and R. delemar strains can be
differentiated by PCR with primers specific to lactate
dehydrogenase (LDH) genes
Abe et al.  demonstrated that R. oryzae contains two copies
of LDH, LDHA and LDHB, whereas R. delemar has only a single
Table 2. Comparison of the number of genes, the length of individual genes, and the length of the entire gene complex in the sex
loci of P. blakesleeanus, M. circinelloides and R. oryzae complex.
Parts of mating type locusP. blakesleeanusM. circinelloides R. oryzae
(+ +)(2 2)(+ +)(2 2)(+ +)(2 2)
GenBank accession #EU009462EU009461 FJ009107FJ009106HQ450315 HQ450316
Total fragment length3
9.977.63 6.88 6.86 13.31 6.96
Intergenic regions, total length3
5.33 3.530.570.883.21 1.5
TPT (EamA-like transporter family)4
BTB domain & ankyrin repeat (RO3G_01289)4
BTB/POZ domain (RO3G_01289)4
Predicted protein, Rcc1 (RO3G_01290)4
HMG (MATA box)4
RNA helicase (RO3G_01291)4
3Length of DNA shown in kilobases.
4Length of protein shown in amino acids.
Table 3. Comparison of the phylogenetic signal obtained
from different genes using different methods for delimitation
of the two cryptic species, Rhizopus oryzae s. s. and Rhizopus
delemar; percent difference is depicted for both DNA (bp) and
amino acids (aa).
mtSSU 370- n. a.-
rDNA 28S 950 0.3n. a.-
5261.7n. a. 83
HMG (2)6323.8 6.299
TPT978 4.15.5 100
RNA helicase7645.1 7.2100
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copy of this gene. We developed PCR primers that amplify
portions of the LDHA and LDHB genes and tested them on 12
isolates from the R. oryzae complex, including six randomly selected
isolates each of R. oryzae s. s. and R. delemar (Fig. 6A). All of the R.
oryzae s. s. isolates produced an amplification product for both
LDHA (ca 500 bp) and LDHB (ca 230 bp). In some cases, a
nonspecific, higher molecular weight PCR product was also
apparent. Sequencing of PCR products of R. delemar isolates
confirmed it as the expected portion of LDHB. For R. delemar only
LDHB products were amplified (Fig. 6B).
Figure 3. Maximum Likelihood phylogenies of the Rhizopus oryzae complex clearly delimit the two cryptic species, Rhizopus oryzae s.
s. and Rhizopus delemar. (A) sexP alleles, (B) sexM alleles, (C) concatenated phylogram of rDNA ITS1-5.8S-ITS2, RPB2, TPT gene, and RNA helicase
gene, and (D) four-gene strict consensus tree. Analysis included a total of 458 (+), 635 (2) and 3064 (MLS) nucleotide characters. ML bootstrap
proportions higher than 70 are shown above the nodes. Asterisks (*) indicate strains that produced zygospores. Filled circles indicate a single R.
delemar strain, CBS329.47, closest to the ancestral state.
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Structure of the sex type locus in the R. oryzae complex
We examined the structure of the putative sex type locus in six
representative strains of R. oryzae and demonstrate that R. ozyzae
possesses a sex type locus that is homologous to those of other
zygomycetes and also of microsporidians. This gene cluster
consists of an HMG domain gene flanked by RNA helicase and
TP transporter genes . The characterization of R. oryzae sex
genes constitutes the third representative of the Mucoromycotina
(Zygomycota) for which the mating gene structure is known. When
compared with the recently described sex loci of P. blakesleeanus and
M. circinelloides, the (+) allele of the R. oryzae sex locus was
significantly larger due to the presence of an additional putative
ORF. However, this inserted gene is absent in the (2) allele of the
locus. Unlike the sex locus of P. blakesleeanus and M. circinelloides,
which contain TPT and HMG genes in inverted orientations, all
genes in the R. oryzae sex type locus were positioned in the same
orientation (Fig. 2). The overall similarity between the sex type
locus of R. oryzae and other zygomycetes was significant, suggesting
that this locus is involved in regulation of the mating process .
Further functional genetic analysis is necessary to confirm this
Cryptic speciation in the Rhizopus oryzae complex
Our phylogenetic analyses confirm the previous observations by
Abe et al. [10,35] that R. oryzae s. l. can be subdivided into two
cryptic species groups, designated R. oryzae s. s. and R. delemar. We
Figure 4. Range of sporangiospore sizes for isolates from the
Rhizopus oryzae complex. Naming convention includes the species
prefix (Ro – Rhizopus oryzae, Rd – Rhizopus delemar) followed by the
strain number. Bars indicate the 95% confidence interval.
Figure 5. Main pattern of asexual sporangiospore micromor-
phology. (A) Rhizopus delemar NRRL3562. (B) R. oryzae NRRL2908.
Arrows show the variation in spore size on the same sporangium
(65000). Scale bar=1 mm.
Figure 6. Different copy numbers of lactate dehydrogenase
(LDH) in Rhizopus oryzae s. s. and Rhizopus delemar. (A) LHDA has a
longer the 39 end compared to LDHB. Primers P1 and P2 recognize both
LDHA and LDHB producing 238 bp DNA fragments in PCR, whereas P3
only recognizes the 39 end of the LDHA producing 525 bp DNA
fragments in PCR with P1. Gene sizes are not to scale. (B) Rhizopus
oryzae s. s. strains produces 238 bp and 525 bp bands in a PCR reaction
with the three primers P1, P2, and P3, however, R. delemar strains
produce only 238 bp bands with the same PCR conditions. Non-specific
amplification of 900 bp bands occurred with several R. oryzae s. s.
strains. Size marker is 100 bp ladder (NEB, Ipswich, MA, USA). Rhizopus
oryzae s. s. strains are (from left to right) NRRL2908, CBS346.36, NRRLA-
336, CBS110.17, NRRL1897, NRRL1501 and Rhizopus delemar strains are
(from left to right) ATCC34612, NRRL2871, NRRL2005, NRRL1528,
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confirmed that the genome strain RA99-880, once thought to
belong to R. oryzae s. s., is actually a member of R. delemar .
Genetic isolation between these two cryptic species was evident in
the strongly supported four-gene phylogeny and the genealogies of
both the (+) and (2) alleles of the HMG genes (Fig. 3). The higher
number of amino acid and nucleotide changes in the sex genes
relative to the ‘‘standard’’ genes (Table 3) suggests that the sex
genes may prove useful in resolving phylogenetic questions in
other zygomycetes and perhaps in other fungi.
Saito et al.  were also able to distinguish R. oryzae s. s. and R.
delemar based on rDNA phylogeny and physiological differences in
acid production. They confirmed the presence of two distinctive
physiological groups: isolates that produce lactic acid and have two
copies of the LDH gene (R. oryzae s. s.) and isolates that produce
both fumaric and malic acids but have only LDHB (R. delemar). We
designed primers for the LDH genes and confirmed a similar
pattern in the 57 isolates we studied. It has been suggested that R.
oryzae’s ability to ferment various organic substrates may explain
why this species was domesticated and used to process various
types of Asian fermented foods [4,11]. Lactate dehydrogenases
(LDH) are important for these enzymatic processes [2,4,11,36,37].
Despite the fact that R. oryzae s. s. and R. delemar can be resolved
by multi-gene phylogenetic analyses and physiological differences
in acid production, morphological examinations and molecular
analyses of more conservative loci indicate that these two cryptic
species are very close relatives. For example, sequences of the
mtSSU and 28S rDNA genes were too highly conserved to provide
any phylogenetic resolution within the R. oryzae complex.
Similarly, analyses of secondary structure in the ITS2 region
indicates that there are no complementary base pair changes
(CBC) between R. oryzae s. s. and R. delemar, whereas other species
in the genus Rhizopus are quite different (Table 4). Furthermore,
isolates of R. oryzae s. s. and R. delemar exhibited similar colony
morphology, growth characteristics, and spore morphology.
Although sporangiospore size is of foremost importance in the
classification of the genus Rhizopus [38,39], spore size measure-
ments were insufficient to distinguish R. oryzae from R. delemar.
Sexual reproduction of R. oryzae and other zygomycetes
in the laboratory and in nature
Fungi employ a variety of reproductive modes, in the lab as well
as in nature. Whereas some fungal species appear to be obligate
sexual organisms (e.g. [40,41]) and others appear to be strictly
asexual [42,43,44], the majority of fungi apparently have a mixed
mating system that includes both sexual and asexual reproduction
(e.g. [45,46,47]). Although earlier studies suggested a predomi-
nantly asexual mode of reproduction in R. oryzae [3,4], analysis of
sequence variation in multiple loci suggests that this species
complex comprises two cryptic species and both exhibit a sexual
mode of reproduction.
Zygospore formation is considered a hallmark of sexual
reproduction. However, only 10% of described Mucoromycotina
species are known to produce zygospores, either under natural
conditions or in pure culture [48,49]. Despite relatively frequent
formation of zygospores in closely related heterothallic (R. stolonifer,
R. microsporus) and homothallic (R. sexualis, R. homothallicus) species,
only a few reports have described zygospore production between
isolates of the R. oryzae complex [3,4,21,25,26]. In our study, 40%
of the isolates of R. oryzae s. s. were capable of producing
zygospores in the laboratory when paired with isolates of the
opposite mating type. The ability to produce zygospores with a
suitable mating partner seems to be characteristic of almost all
subgroups of the R. oryzae s. s. clade (Fig. 3).
Most strains producing zygospores in our study belong to the R.
oryzae s. s. clade (Table S3). Although most isolates of R. oryzae s. s.
were capable of producing zygospores, we observed that their
morphology was more similar to the azygospores observed in other
zygomycetes. Zygospores of R. oryzae possess asymmetric suspen-
sors of unequal size, a feature associated with azygospore
production in R. stolonifer and R. azygosporus [3,6,18,19]. Single
asymmetric suspensors have been reported in different varieties of
R. microsporus , and in distantly related species from the genera
Absidia and Zygorhynchus . In the genus Rhizopus, zygospore
formation may not be a useful character for delimiting species
boundaries because many Rhizopus isolates form zygospores even
when their mating partner belongs to a different species .
In our study, R. oryzae zygospores did not germinate into
germosporangia  under any of the tested experimental
conditions. When zygospores were mechanically disrupted, the
multinuclear protoplast developed into a vegetative mycelium that
contained nuclei of only the (2) mating type, indicating that
meiosis did not occur. If meiosis had occurred, we would instead
expect equal proportions of (+) and (2) mating types. This result
suggests that mating and recombination might not occur under
In contrast, zygospores of the closely related species R. stolonifer
can germinate in two different ways. When zygospores are
geminated prior to maturation, they form a vegetative mycelium
that is either (+) or (2). When mature zygospores are germinated,
they form a germosporangium that produces spores with equal
proportions of (+) and (2) mating types [25,26,49]. Germination
of zygospores into vegetative mycelia is also known in distantly
related species in the genus Zygorhynchus .
Although we did not directly detect successful mating and
progeny development in the laboratory, we did observe nearly
equal frequency of (+) and (2) mating types across both cryptic
species within the R. oryzae species complex (Table S3). This
provides strong indirect evidence for sexual recombination in R.
oryzae. Analysis of multiple gene phylogenies provides further
evidence for outcrossing. Phylogenetic analyses of individual and
combined loci consistently support two well-defined sibling species,
R. oryzae s. s. and R. delemar. Within each species, however,
discordant gene trees suggest that both species are inherently
sexual, with an outcrossing mode of reproduction (Fig. S1,
supplementary materials). If populations of each species were
clonal, we would expect independent gene trees to be concordant
. In this study, we consistently observed conflict between gene
partitions within both species (ph test, p,.001), suggesting
Table 4. Analysis of similarity between Rhizopus oryzae s. s.
and other Rhizopus species in ribosomal DNA sequences
(ITS1-5.8S-ITS2, 28S) and predicted compensatory base
changes (CBC) for the ITS2 region.
rDNA ITS1-5.8S-ITS2rDNA 28S CBC
R. delemar 98.3% (HQ435103)99.7% (HQ435039) 0
R. microsporus65% (HQ450314) 95% (HQ435046)2
R. homothallicus68% (EU491016)94% (DQ641324)2
R. azygosporus43% (DQ641314) 93% (DQ466597)2
R. caespitosus43% (DQ641325) 93% (DQ466604)2
R. schipperae 43% (DQ641323)92% (DQ466606)2
R. sexualis 55% (DQ641322)89% (DQ466592)8
R. stolonifer39% (FN401529) 89% (DQ466595)6
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recombination between loci. Together with equal distribution of
sexes, our results strongly support the hypothesis that genetic
recombination is occurring within both R. oryzae s. s. and R. delemar.
Further studies employing population-level sampling, along with
genome sequencing of R. oryzae s. s. will be necessary to determine
the extent and nature of recombination in both species.
Mucormycosis is an emerging infectious disease  and is
increasingly reported as a cause of fungal infection in patients with
impaired immunity . Isolates from the R. oryzae complex are
the most common zygomycetes infecting humans [54,55]. Our
phylogenetic studies also suggest that the two cryptic species, R.
delemar and R. oryzae, may differ in relative virulence. It is also
possible that R. delemar and R. oryzae may differ in susceptibility to
antifungal drugs [55,56]. In the pathogenic basidiomycete,
Cryptococcus neoformans, the MAT locus is linked to virulence
[57,58]. It is possible that the sex locus might be similarly involved
in the pathogenesis of Rhizopus species.
Our data support the hypothesis that the genetic machinery for
sexual reproduction is conserved among multiple genera of
Mucoromycotina. Rhizopus oryzae is one of the most economically
important members of this group. Our multi-gene phylogenetic
analyses support the existence of two cryptic species: R. delemar and
R. oryzae. Notably, the recently sequenced genome isolate is a
member of R. delemar, so it would be ideal to also sequence a
representative genome of R. oryzae s. s. We demonstrate that both
species have the potential for sexual reproduction, and although
our mating studies suggest that sexual reproduction is infrequent,
strains of both mating types are equally abundant in both species.
Materials and Methods
Cultivation of fungal strains
Strains of Rhizopus oryzae s. l. were obtained from different
culture collections: American Type Culture Collection (ATCC),
Duke University, Fungal Genetics Stock Center (FGSC), Agricul-
tural Research Service Culture Collection (NRRL) in USA,
Centraalbureau voor Schimmelcultures (CBS) in the Netherlands
and Friedrich-Schiller University Fungal Reference Center in
Germany (Table S3). Replicate isolates of several mating type
tester strains first described for R. oryzae by Schipper  were
included. Strains were grown on 10% Potato-Dextrose Agar
(PDA) (NEOGEN, Lansing, MI, USA), in tubes and 90 mm Petri
plates at room temperature.
Light microscopy and fungal morphology
Wet mounts of asexually sporulating isolates were examined at
100–4006under an Olympus CX31 lightmicroscope equipped with
an ocular micrometer (Olympus America Inc., Center Valley, PA,
USA). To test whether morphology could be used to differentiate
genetically related strains within the R. oryzae complex we made 100
chosen strains (Fig. 4). We then analyzed the morphology and size of
R. oryzae s. l. spores using multivariate discriminate analysis and
cluster analysis [59,60,61]. The following statistical parameters were
examined for asexual sporangiospore dimensions: average (M),
variance (D), standard deviation (s), and standard error (6m). All
statistical analyses were conducted in the STATISTICA 6.0software
package (StatSoft Inc., Tulsa, OK, USA).
Mating tests were conducted in 4.5 or 9 cm diameter Petri
plates with several types of standard agar growth media: PDA,
Malt Agar (MA) (VWR International, Bristol, CT, USA), Glucose
Peptone Yeast Extract Agar (GPYA) (HiMedia Laboratories Pvt.
Ltd., Mumbai, India), Sabouraud agar , and water agar .
Mating tests were conducted at three different nutrient levels;
10%, 50%, or 100% of the level recommended by the
manufacturer to test the affect of nutrients on zygospore
germination. Petri plates were either inoculated with 161 cm
agar pieces taken from the growing edge of the colony, or with a
20 ml suspension of lyophilized tissue. In each mating test inocula
from two isolates were placed 1 cm from each other on a fresh
Petri plate. Cultures were then incubated in either complete
darkness or exposed to light and they were either sealed or not
sealed with Parafilm (Pechiney Plastic Packaging, Menasha, WI,
USA) at room temperature according to Hesseltine and Rogers
. Development of conjugating hyphae and zygospores was
observed at 100–4006under an Olympus CX31 light microscope
(Olympus America Inc., Center Valley PA, USA) or at 200–
35006with a JSM-5900LV scanning electron microscope (SEM)
(JEOL U.S.A., Peabody MA, USA). Observations for mating were
conducted several times each week for a period of 6–8 weeks. For
mating crosses that produced zygospores, we attempted to
stimulate germination following traditional protocols . We
also tested whether it was possible to grow ungerminated
zygospores by crushing them with forceps and then incubating
them on nutrient agar.
DNA extraction, amplification and sequencing
Prior to DNA isolation cultures were incubated for 8 to
20 hours at room temperature in 50 ml of Potato Dextrose broth
(NEOGEN, Lansing, MI, USA) and were then filtered through a
sterilized Mira cloth . Mycelium was then lyophilized for 1 to
2 days and ground in liquid nitrogen with a mortar and pestle or
DNA was extracted following the CTAB extraction technique
. PCR mixtures with a total volume of 25 ml per sample were
prepared according to the protocol supplied by TaKaRa (TaKaRa
Bio Inc., Otsu, Shiga, Japan). PCR was performed according to
the basic protocols outlined by White et al.  for all genes except
where specifically noted below. The internal transcribed spacer
region of rDNA (ITS1-5.8S-ITS2) was amplified with primers
ITS1 and ITS4 . Partial large subunit rDNA 28S was
amplified using the primers LROR  and LR5 . The
mitochondrial SSU was amplified with the primer set mtSSU1_f
and mtSSU2_r . The genome of R. oryzae has two non-
identical copies of RPB2 located on different supercontigs.
Accordingly, it was not possible to use the coding domains 5–7,
which are located in the central part of the gene and have
traditionally been used in fungal phylogenetics. To overcome this
problem, we obtained DNA sequences of coding domains 1–3,
which are unique to the RPB2 copy located on Supercontig 10. To
amplify the 59 end (domain 1, intron 1 and part of domain 2) of
the RNA Polymerase II subunit 2 gene (RPB2), we designed three
new primers (Rh_RPB2_f, Rh_RPB2l_r and Rh_RPB2s_r –
Table S1) using the RPB2 sequence from the R. oryzae genome
database. For RPB2 a ‘‘touchdown’’ PCR protocol was used as
described by Don et al. .
All PCR-amplified fragments were separated by electrophoresis
on a 1.5% agarose gel stained with SYBRH Safe and visualized
with a UV transilluminator. PCR products were purified with
Qiagen Quick-Clean columns (Qiagen Inc., Valencia, CA, USA)
or with ExoAP enzymes . PCR products were then sequenced
using amplification primers and Big Dye chemistry version 3.1
(Applied Biosystems Inc., Foster City, CA, USA), and the DNA
sequences were run on an ABI3700 DNA sequencer (Applied
Mating Locus in Rhizopus oryzae
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Biosystems Inc., Foster City, CA). DNA sequences generated for
this study were edited in Sequencher 4.0 (Gene Codes, Ann Arbor,
MI, USA), and are available in GenBank (Table S2).
We characterized rDNA 28S and ITS1-5.8S-ITS2, mtSSU,
HMG, RPB2, TPT, and RNA helicase genes for 41 isolates
(Table 3). We also examined the phylogenetic pattern of the
‘‘plus’’ and ‘‘minus’’ mating alleles to see whether these regions
could be used to distinguish between different lineages from the R.
oryzae complex. First, we compared the phylogenetic signal of the
‘‘plus’’ and ‘‘minus’’ alleles to other genes that have traditionally
been used for phylogenetic analyses of fungi (rDNA 28S and ITS1-
5.8S-ITS2, RPB2). Next, we compared the phylogenetic signal of
the ‘‘plus’’ allele with the ‘‘minus’’ allele to see if inferences from
each of these alleles were similar and which region was more
informative. Phylogenetic relationships were determined by
Maximum Likelihood (ML) and phylogenetic support was assessed
for each gene by bootstrap analyses (ML) using PAUP* 4.0a109
. Using sequences of rDNA ITS1-5.8S-ITS2, RPB2, TPT, and
the RNA helicase genes, the maximum likelihood approach was
applied to generate a four genes tree for all of the 41 studied
isolates. The partition homogeneity test was run on PAUP*
4.0a109 using a parsimony criterion for four genes and 1000
After characterizing the sex genes of several R. oryzae isolates, we
compared them to the previously characterized sex alleles of
Phycomyces blakesleeanus (EU009461, EU009462) and Mucor circinel-
loides (FJ009106, FJ009107). Nucleotide and amino acid similarity
of HMG, TPT and RNA helicase gene/protein alignments was
examined in Multalin  and ClustalW2 .
To generate a dataset of Rhizopus reference taxa, additional
rDNA 28S and ITS1-5.8S-ITS2 sequences from identified
Rhizopus species with accurate nomenclature were either down-
loaded from GenBank or generated in this study (Table 4) .
Compensatory base changes in the ITS2 region for Rhizopus
species were calculated using the ITS2 Database and the programs
4Sale and CBCAnalyzer [74,75,76,77]. We did not detect any
compensatory base changes between R. oryzae and R. delemar in the
ITS2 region (Table 4).
All sequences were initially aligned in ClustalX . Align-
ments were manually adjusted and ambiguous regions were
excluded from the alignments using Mesquite 2.5 . sex loci and
other genes of the strains of interest were aligned and compared
using Sequencher 4.0 (Gene Codes, Ann Arbor, MI, USA),
Multalin  and ClustalW2 .
Repetitive sequences in ‘‘plus’’ and ‘‘minus’’ alleles of the sex
locus were determined manually and using the Tandem Repeats
Finder . Inverted and palindromic repeats were identified
using tools available at the REPEATS, SECONDARY STRUC-
TURE & MELTING TEMPERATURE web site (http://emboss.
bioinformatics.nl/cgi-bin/emboss/). Directionality of the genes in
the sex loci was determined in ORF Finder (www.ncbi.nlm.nih.
gov/gorf/) and displayed with a dot plot.
Analysis of mating genes
Primers for the TPT and RNA helicase flanking genes were
designed using Primer3  from the R. oryzae database sequences.
PCR reactions using these primers were conducted using the
TaKaRa protocol (TaKaRa Bio Inc., Otsu, Shiga, Japan).
Products were isolated and purified using a gel extraction kit
(Qiagen GmbH, Hilden, Germany), cloned with a TOPO TA kit
(Invitrogen, Carlsbad, CA, USA), and sequenced as described
above. New primers were subsequently designed at the end of the
newly sequenced region and the process was repeated by ‘‘primer
walking’’ to obtain DNA sequences between the flanking genes. A
total of fifty-seven primers were employed to sequence the entire
length of the Rhizopus sex locus, including the flanking genes (Table
S1). The entire sex locus and the two flanking regions were
sequenced for five strains (Table 2) and these data were used to
design primer sets for direct amplification of the mating loci:
SgeneCORE_for and SgeneCORE_rev for the ‘‘minus’’ allele and
Plus1_f and Plus1_r for the ‘‘plus’’ allele (Table S1). PCR with the
SgeneCORE primer set produced a fragment of 780–800 bp
whereas PCR with the Plus1 primer set produced a fragment of
465–480 bp. To avoid formation of secondary structures during
amplification of intergenic regions of the sex locus, 1% DMSO was
added to both PCR and sequencing mixtures .
Use of the Lactate Dehydrogenase (LDH) gene to
differentiate R. oryzae sensu stricto from R. delemar
Lactate dehydrogenase genes encode hydrolytic enzymes that
enable R. oryzae to grow in decaying organic matter rich in
complex carbohydrates . Previous research has shown that
differences in the LDH genes can differentiate R. delemar from R.
oryzae s. s. Rhizopus delemar has only one copy of the gene (LDHB)
whereas R. oryzae s. s. has two copies (LDHA and LDHB) [11,14]
(Rhizopus oryzae database). The sequences of these two genes are
almost identical except that LDHA has a longer 39 ORF. Although
we did not include this locus in our phylogenetic analyses, we
developed a PCR-based method to efficiently distinguish between
R. oryzae s. s. and R. delemar using a combination of one forward
and two reverse primers for the LDH gene. The forward primer
JOHE22917 anneals to both genes. The reverse primer
JOHE22918 anneals to both LDHA and LDHB whereas the other
reverse primer JOHE22919 recognizes only LDHA (Fig. 6A).
When PCR is performed with all three primers, R. oryzae s. s.
isolates yield two fragments of different sizes: one PCR product for
LDHA and another for LDHB. Isolates of R. delemar yield only one
PCR product, however. We randomly selected six strains each of
R. oryzae s. s. and R. delemar to test the LDH PCR assay. Results
were compared with phylogenetic analyses used to distinguish
5.8S-ITS2 (A), RPB2 (B), TPT (C) and RNA helicase (D) genes.
Analysis included a total of 566 (rDNA ITS1-5.8S-ITS2), 757
(RPB2), 978 (TPT) and 764 (RNA helicase) nucleotide characters.
ML bootstrap proportions higher than 70 are shown above the
nodes. Group * includes ITS sequences AB097299, AB181316-
AB181330 of Rhizopus delemar; group ** includes the ITS sequences
AB181303-AB181309, AB181311-AB181315, AB097334 of Rhi-
zopus oryzae . T – type culture of R. oryzae s. s., T’ indicates a
strain with an rDNA ITS1-5.8S-ITS2 sequence that is identical to
the type culture of R. delemar (CBS120.12).
Maximum Likelihood phylogeny for rDNA ITS1-
spores of Rhizopus oryzae. (A) Electron micrograph of a cross
between R. oryzae strains CBS346.36 6 CBS110.17 showing
zygospores (black arrow heads). Scale bar = 50 mm. (B) Asexual
sporangium of R. delemar strain NRRL3563 without sporangium
wall. Scale bar = 20 mm. (C) Germinating of zygospore’s
protoplast (white arrow) into vegetative mycelium after crushing
of lateral spore wall (black arrows). Scale bar = 50 mm. (D)
Different size of uni- (black arrow) and binucleate (white arrow)
Sexual (zygospores) and asexual (sporangiospores)
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DAPI stained sporangiospores of Rhizopus delemar RA99-880. Scale
bar = 20 mm.
Rhizopus delemar (from top to bottom): ATCC34612, RA99-880,
NRRL3562. Panel B) Rhizopus oryzae s. s.(from top to bottom):
NRRL2908, Duke99-133, NRRL3142. Panel C) Germination of
the Rhizopus oryzae s. s. strain, CBS112.07. Scale = 1 mm for panel
A and B, and 5 mm for panel C.
Micromorphology of sporangiospores. Panel A)
List of primers designed in this study.
generated in this study.
GenBank accession numbers of the sequences
species used in this study; isolates of Rhizopus oryzae and Rhizopus
delemar are named according to their placement in phylogenetic
trees (See Results).
Isolates of the Rhizopus oryzae complex and related
We thank Kerry O’Donnel, Wiley Shell, Ashraf Ibrahim and Andrej
Gregory for R. oryzae isolates; Tom Mitchell, Franc ¸ois Lutzoni, John Shaw,
William Colquhoun, Bernie Ball, Sandra Boles, Kerstin Hoffmann, Tami
McDonald, Kathleen Miglia, Katalin Molnar, Heath O’Brien, Hannah
Reynolds, Bernadette O’Reilly, Marianela Rodrigues-Carres, Peter
Szovenyi, Kerstin Voigt, Ninel Terentyeva, Oleksandr Savytskyi, Ninel
Gurinovich and Grit Walter for advice on experimental work, figure
design, statistical and data analyses; Iryna Dudka, Richard Humber and
Christopher Skory for experimental ideas and morphological information
on R. oryzae; Mary Berbee, Tim James, Asia Buchalo, Reinhold Po ¨der,
Blanka Shaw, Jason Jackson, Sarah Jackson and Cathie Aime for essential
discussions; Lisa Bukovnik for sequence analysis; Sheri Frank for reagent
and culture supply; Jolanta Miadlikovska, Bernie Ball and Suzanne Joneson
for help with primer design and sequence analysis; Valerie Knowlton for
SEM assistance, and Scarlett Geunes-Boyer for considerable text
Conceived and designed the experiments: AG SCL RV JH. Performed the
experiments: AG SCL APL TMP GB. Analyzed the data: AG SCL APL
MES GB TMP IMA JH RV. Contributed reagents/materials/analysis
tools: JH RV. Wrote the paper: AP SCL JH RV.
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