Fungal Diversity (2011) 50:189–225
DOI 10.1007/s13225-011-0126-9
The genus Phomopsis: biology, applications, species
concepts and names of common phytopathogens
Dhanushka Udayanga & Xingzhong Liu &
Eric H. C. McKenzie & Ekachai Chukeatirote &
Ali H. A. Bahkali & Kevin D. Hyde
Received: 21 June 2011 / Accepted: 22 July 2011 / Published online: 6 September 2011
# Kevin D. Hyde 2011
Abstract The genus Phomopsis (teleomorph Diaporthe)
comprises phytopathologically important microfungi with
diverse host associations and a worldwide distribution.
Species concepts in Phomopsis have been based historically
on morphology, cultural characteristics and host affiliation.
This paper serves to provide an overview of the current
status of the taxonomy in Phomopsis with special reference
to biology, applications of various species, species concepts, future research perspectives and names of common
pathogens, the latter being given taxonomic reappraisal.
Accurate species identification is critical to understanding
disease epidemiology and in developing effective control
measures for plant diseases. Difficulties in accurate species
identification using morphology have led to the application
of alternative approaches to differentiate species, including
D. Udayanga : X. Liu
State Key Laboratory of Mycology, Institute of Microbiology,
Chinese Academy of Sciences,
No 3 1st West Beichen Road, Chaoyang District,
Beijing 100101, People’s Republic of China
D. Udayanga : E. Chukeatirote : K. D. Hyde (*)
School of Science, Mae Fah Luang University,
Thasud,
Chiang Rai 57100, Thailand
e-mail: kdhyde3@gmail.com
E. H. C. McKenzie
Landcare Research,
Private Bag 92170,
Auckland, New Zealand
A. H. A. Bahkali : K. D. Hyde
College of Science, Botany and Microbiology Department,
King Saud University,
Riyadh, Saudi Arabia
virulence and pathogenicity, biochemistry, metabolites,
physiology, antagonism, molecular phylogenetics and mating experiments. Redefinition of Phomopsis/Diaporthe
species has been ongoing, and some species have been
redefined based on a combination of molecular, morphological, cultural, phytopathological and mating type data.
Rapid progress in molecular identification has in particular
revolutionized taxonomic studies, providing persuasive
genetic evidence to define the species boundaries. A
backbone ITS based phylogenetic tree is here in generated
using the sequences derived from 46 type, epitype cultures,
and vouchers and is presented as a rough and quick
identification guide for species of Phomopsis. The need
for epitypification of taxonomic entities and the need to use
multiple loci in phylogenies that better reflect species limits
are suggested. The account of names of phytopathogens
currently in use are listed alphabetically and annotated with
a taxonomic entry, teleomorph, associated hosts and disease
symptoms, including brief summaries of taxonomic and
phylogenetic research. Available type culture information
and details of gene sequences derived from type cultures
are also summarized and tabulated.
Keywords Anamorph . Antagonism . Biocontrol . Canker .
Chemotype . Endophyte . Epitypification . Genetic
transformation . Mating type . Molecular phylogeny .
Pathogen . Morphology . Mycotoxins . Quarantine
Introduction
Phomopsis (Sacc.) Bubák is an important phytopathogenic
genus in urgent need of taxonomic reappraisal (Rehner and
Uecker 1994; Farr et al. 2002a, b; Cristescu 2003; Murali et
190
al. 2006; Hyde et al. 2007; Santos et al. 2010; Cai et al.
2011). This is because micromorphology and phylogenetic
characters add an extra level of resolution to the host-based
identification previously used (Zhang et al. 1997, 1999;
Murali et al. 2006; Santos and Phillips 2009; Santos et al.
2010; Diogo et al. 2010). The genus Phomopsis (anamorph
of Diaporthe Nitschke) contains more than 900 species
names from a wide range of hosts (Uecker 1988; Rehner
and Uecker 1994; Crous 2005; Mostert et al. 2000;
Rossman et al. 2007; Rossman and Palm-Hernández 2008).
The objectives of this review of Phomopsis are to (1)
evaluate the current problems of taxonomy and nomenclature; (2) review the biology, life styles and applications of
species of the genus (e.g. biological control, secondary
metabolites); (3) discuss taxonomic research and species
concepts; (4) speculate the need of advancement of
understanding of the genus and future trends of research,
and (5) provide a compilation of names of common
phytopathogens in current use.
Nomenclatural history
The precise naming of organisms is crucial, since the name
is the key to access all accumulated knowledge concerning
each organism (Hawksworth and Rossman 1997; Hawksworth 2011). The occurrence of dual or multiple morphological forms of a fungal species (i.e. pleomorphism) and
the dual nomenclature system used in the classification of
classification of fungi has resulted in difficulties in
developing a natural system of classification of fungi and
a confusion in names (Shenoy et al. 2010). For these
reasons a stable nomenclatural system with a single precise,
clearly defined name for species is essential for all aspects
of scientific study.
The name Phomopsis in its first documented records was
applied to anamorphs of nectriaceous fungi, with several
changes over time in its nomenclatural status (Uecker
1988). Phomopsis became more stable when Saccardo
(1883) defined Phomopsis as a group of Phoma species
that produced beta-conidia, but he did not transfer any
species to Phomopsis. Later in the same volume of Sylloge
Fungorum (Saccardo 1884) treated P. versoniana and P.
brassicae as species of Zythia. The present sense of the
name Phomopsis (Sacc.) Bubak. (1905) resulted from the
transfer of Phoma lactucae Sacc. to Phomopsis. Later, in
the same year Saccardo (1905) raised Phomopsis to generic
rank and listed two species- Phomopsis lamii Sacc. and P.
pritchardiae (Cooke & Harkn.) Sacc. Saccardo (1906)
transferred three species of Myxolibertella to Phomopsis,
while Höhnel (1906) agreed that Phomopsis and Libertella
were the same and he used only Phomopsis in his writings
(Uecker 1988).
Fungal Diversity (2011) 50:189–225
Diaporthe Nitschke is the sexual state of Phomopsis
with more than 800 names included in Index fungorum
mostly independent of any anamorphic affinities. Since
only 20% of anamorphic teleomorph connections are
resolved for this genus, the need to link anamorphs with
their teleomorphs using molecular data has been proposed
(Sutton 1980; Rehner and Uecker 1994; Chi et al. 2007;
Hyde et al. 2011). Riedl and Wechtl (1981) formally
proposed the conservation of the name Phomopsis and this
was accepted at the International Botanical Congress in
1987 and the need of lectotypification with Phomopsis
lactucae (Sacc.) has been emphasized (Uecker 1988).
Wehmeyer (1933) in his comprehensive treatment of Diaporthe used morphology to differentiate the teleomorph and
the asexual state was not considered. However, Chi et al
(2007) used Phomopsis as the preferred generic name in the
Chinese compilation of over 200 species of Phomopsis.
Diaporthopsis Fabre (1883) was described as a genus that
is similar to Diaporthe but distinguished by non-septate
ascospores. The type species of Diaporthopsis, Diaporthe
angelicae (Berk.) Farr & Castl. was transferred to Diaporthe
based on molecular and morphological data and therefore
Diaporthopsis is now considered as a synonym of Diaporthe
(Castlebury et al. 2003).
Diaporthe or Phomopsis—which name should be used?
There is a movement underway to provide all fungal
species with a single name instead of the present practice of
providing a teleomorph and anamorph name for the different
states of a species (Shenoy et al. 2007; Hawksworth 2011;
Hyde et al. 2011). The use of two names for a species is
both confusing and unnecessary and has been the product of
the dual nomenclature system (Shenoy et al. 2007). Several
arguments have been made in the taxonomic history of
Diaporthe/Phomopsis regarding the use of names of the
teleomorph and anamorph states (Chi et al. 2007, Santos et
al. 2010).
Since we are now able to link anamorph and teleomorph
states through molecular sequence data regardless of whether
the taxon in question expresses sexual or asexual structures
the need for a binomial system is becoming redundant
(Shenoy et al. 2007, 2010; Gehlot et al. 2010; Hawksworth
2011). However, in moving forward to using one name to
represent the sexual and asexual states of a biological species
many difficulties have to be overcome (Shenoy et al. 2010;
Hyde et al. 2011).
In Diaporthe/Phomopsis we have the option of using the
sexual name (Diaporthe), the older name (Diaporthe-1870
versus Phomopsis-1905), the name that is most often
applied to important disease-causing organisms (i.e.,
Phomopsis), or maintaining the status quo as Diaporthe
and Phomopsis. Santos and Phillips (2009) proposed to
Fungal Diversity (2011) 50:189–225
give preference to the older Diaporthe (1870) names, rather
than the younger anamorphic genus, Phomopsis (1905),
discouraging the introduction of separate anamorph names
for new species of Diaporthe in current investigations.
In this review we opt to use the anamorph name based
on the fact that this state is most common in nature and
it is also applied to many important diseases. Therefore,
herein we generally use Phomopsis to represent both
Phomopsis and Diaporthe species, unless we clearly want
to distinguish between two morphs.
The use of the bionomial system in Diaporthe/Phomopsis
can result in considerable confusion and we detail several
examples where confusion using two anamorph-teleomorph
names for identical taxa has resulted and some advantages of
using a single name. For instance, Phomopsis vitimegaspora
Kuo & Leu associated with dead arm disease of grapevines
in Taiwan was identified by Kuo and Liu (1998). The
teleomorph was later recognized from Kyushu, Japan and
designated the name Diaporthe kyusuensis Kajitani &
Kanematsu with ITS sequence similarities (Kajitani and
Kanematsu 2000). Thus the same species has two completely
different names. Two varieties of Phomopsis (P. leptostromiformis var. leptostromiformis (J.G. Kühn) Bubák, and P.
leptostromiformis var. occidentalis Shivas) were identified as
causing disease in Lupinus sp. Diaporthe woodi Punith. was
later recognized as the teleomorphic state of P. leptostromiformis var. occientalis (Punithalingam 1974), while
Williamson et al. (1994) designated the name Diaporthe
toxica P.M. Will., Highet, W. Gams & Sivasith. for the
teleomorph of the toxicogenic variety of P. leptostromiformis var. leptostromiformis. In these, two examples
more than one name represents a single species (based on
the dual system of classification). Now as it is easier to
link names using molecular data, one preferred name is
needed in future understanding of a species.
The use of two names to represent species recorded from
one host has introduced much confusion. For instance,
Phomopsis viticola Sacc. and allied species of Phomopsis
associated with grapes are have been reassessed in several
studies (Merrin et al. 1995; Phillips 1999, 2000; Mostert et
al. 2001a). Phomopsis viticola is however, regarded as a
anamorphic species as the sexual stage is not yet formed in
recent studies, despite the amplification of both of mating
type genes in different isolates (Santos et al. 2010).
Cryptosporella viticola Shear is now used as a synonym
for P. viticola, which was previously thought to be the
teleomorph. The names Diaporthe austalafricana Crous &
Van Niekerk, D. viticola Nitschke and D. perjuncta Niessl
have been given to the other taxa identified from grapevines. Several different Phomopsis taxa (Phomopsis sp. 1 to
8) from grapevines were identified on basis of ITS and
morphological data and not identified to species level due
to the doubtful nature of host range or the frequency of
191
occurrence (van Niekerk et al. 2005). All records from
grapes in this complex however, should belong to one
genus (i.e., Phomopsis) although the existing nomenclatural
system has made the situation confusing.
The existence of homothallic and heterothallic taxa and
compatible mating groups among species of this genus have
been identified and confirmed by MAT gene-based rational
selection and conventional mating experiments (Kanematsu et
al. 2007; Santos et al. 2010). Therefore, current knowledge
supports the recognition of taxa within a biological and
phylogenetic framework congruent with the linking of
anamorphic and teleomorphic states. An attempt to use a
single name for genetically identical taxa is workable. The
significance of mating types of Phomopsis and other related
concepts are discussed under the section of sexual state,
mating types and molecular basis of mating experiments.
Several important changes to the naming of fungi and
needs to be further clarified. However, where anamorph and
teleomorph names are involved, the oldest name will have
priority unless a more commonly used name is conserved
over the older name. Thus, Diaporthe is the oldest name
and has priority over Phomopsis and Diaporthe should be
used for all Phomopsis species. Although Phomopsis is
generally the more commonly used name it could not be
used unless it was conserved over Diaporthe and as we
understand this is a lengthy process.
Life modes of Phomopsis
Species of Phomopsis have been reported as plant pathogens,
endophytes, saprobes and even causing health problems in
humans and other mammals (Van Warmelo et al. 1970; Uecker
1988; Rehner and Uecker 1994; Sutton et al. 1997; GarciaReyne et al. 2011). Several species isolated as pathogens of
crops also have been isolated as endophytes from healthy
tissues of the same or different hosts and also as saprobes from
dead material (Promputtha et al. 2007; Udayanga et al. 2011).
Diaporthe helianthi Munt.-Cvetk., a pathogen associated
with the diseases of sunflower has been reported from
pruning debris of Vitis vinifera in South Africa (van Niekerk
et al. 2005). In the same study, Phomopsis amygdali (Delacr.)
Tuset & Portilla, a pathogen associated with shoot blight of
almond and peach has been recorded from the asymptomatic
nursery plant of Vitis vinifera in South Africa. In another
case, D. phaseolorum, the causative agent of diseases of
soybean has been reported as endophytes in the estuarine
mangrove plant Kandelia candel (Cheng et al. 2006).
Phomopsis as a pathogen
Species of Phomopsis cause cankers, diebacks, root rots,
fruit rots, leaf spots, blights, decay and wilts on a wide
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Fungal Diversity (2011) 50:189–225
Fig. 1 Diseases caused by
Phomopsis species on economically important crops:
A Phomopsis cane spot of
grapevines caused by P. viticola.
B Phomopsis leaf spot by P.
viticola, C Stem canker of sunflower caused by Phomopsis
helianthi, D Twig canker on
Prunus persica (peach) caused
by P. amygdali E Soybean field
infected with Diaporthe phaseolorum. F Stem canker of soybean
caused by D. phaseolorum.
Picture credits: A, B Dr. Belinda
Rawnsley, South Australian
Research and Development
Institute (SARDI), Australia,
D Dr. Sam Markell, North Dakota State University, USA.
D Dhanushka Udayanga, Mae
Fah Lunag University, Thiland/
Chinese Academy of Sciences,
Beijing. E, F Dr. Thomas Chase,
South Dakota University, USA
range of plant hosts (Fig. 1) including some economically
important hosts worldwide (Uecker 1988; Santos and
Phillips. 2009) and have been the subject of considerable
phytopathogen research (Meyer et al. 2009; Li et al. 2010a,
b; Hyde et al. 2010a, b; Nagendra Prasad et al. 2011). There
has however, been no general review of this important
pathogenic group. We do not discuss the phytopathogenic
species of Phomopsis further here in; however, most of
them are included in a latter section in this paper with
names of phytopathogens annotated with partucular hosts
and information on the diseases involved.
Most species of Phomopsis are thought to be hemibiotrophs. Biotrophic fungi require living plants as a source
of nutrients, while necrotrophic fungi kill their hosts and
live off the dead tissue (Berger et al. 2007). When the host
is infected by a necrotrophic pathogen, the plant suffers
severe effects, and the pathogen continues to survive on the
host as a saprobe following tissue death (van Kan 2006),
living on the nutrients from the tissue they have killed.
Phomopsis pathogens are nectrotrophic at least for the
latent phase of infection and are therefore called hemibiotrophs (Rosskopf et al. 2000b).
Fungal Diversity (2011) 50:189–225
Despite their significance as destructive plant pathogens,
some species of Phomopsis such as P. leptostromiformis
which infects lupines (Lupinus spp.), also cause lupinosis, a
type of mycotoxicosis in sheep which follows consumption
of diseased plants (Van Warmelo and Marasas 1972). The
report of the occurrence of Human Phaeohyphomycotic
Osteomyelitis (a subcutaneous infection of a finger of
immunosuppressed female) by a species of Phomopsis
resulted in the addition of Phomopsis to the list of
coelomycetous fungi capable of causing human diseases
(Sutton et al. 1999). Phomopsis longicolla Hobbs was also
reported from a human cutaneous infection in an immunosuppresssed renal transplant recipient from Guinea; the
organism was previously known as a phytopathogen on
soybean seeds (Garcia-Reyne et al. 2011).
Phomopsis as endophytes
Species of Phomopsis are prevalent as endophytes of
many hosts in both temperate and tropical regions and
are especially common in the sapwood of angiosperms
(Bussaban et al. 2001; Tomita 2003; Rossman et al. 2007;
Murali et al. 2006; Suryanarayanan et al. 2002; Botella
and Diez 2011; González and Tello 2011). Endophytic
species of Phomopsis were present in the sapwood of
almost all angiosperm endophytes examined by Boddy
and Griffith (1989). Promputtha et al. (2005) reported that,
from a total of 31 morphospecies of sterile endophytes
from Magnolia liliflora (Magnoliaceae) identified based
on molecular phylogeny, 24 were Phomopsis species; this
finding has been corroborated in several other recent
studies with different hosts (Murali et al. 2006; Chaeprasert et al. 2010; Rocha et al. 2011; Sun et al. 2011;
Udayanga et al. 2011).
The potential role of endophytes in protecting plants
from fungal diseases such as Dutch elm disease has been
explored (Brayford 1990). An endophytic Phomopsis sp.
from living bark of Cavendishia pubescens in Colombia
produced paspalitrem A and paspalitrem C in batch
fermentations. These compounds previously were known
only from sclerotia of Claviceps paspali as tremorgenic
mycotoxins causing neurological disorders of livestock
(Bills et al. 1992). Thus the presence of endophytes in
plant may be advantageous for the plants and may deter
herbivory (Brayford 1990; Hyde and Soytong 2008; Weber
2009; Vesterlund et al. 2011).
Phomopsis as saprobes
There are abundant records species of Phomopsis as
saprobes on decaying hosts, as well as latent endophytes
and pathogens becoming early colonizers on wide range of
decaying host materials (Promputtha et al. 2007; Kodsueb
193
et al. 2008a, b; Kumaresan and Suryanarayanan 2002;
Osono and Takeda 2002; Yanna and Hyde 2002; Hyde et
al. 2007; Promputtha et al. 2010). Nine endophyte strains
were isolated from leaves of Magnolia liliflora and three
of them were Phomopsis which are morphologically and
phylogenetically similar to saprobes isolated from the early
decay stage of leaves of the same host (Promputtha et al.
2010). Endophytic Phomopsis strains have also been shown
to produce leaf degrading enzymes similar to those of
saprobic strains which support the biochemical evidence that
endophytes become saprobes at leaf senescence (Promputtha
et al. 2010; Dai et al. 2010; Meenavalli et al. 2011).
Potential applications of Phomopsis
Ceolomycetous fungi also have gained the attention in the
discovery of novel biochemically and physiologically active
compounds and their direct use in agricultural biotechnology
and medicine (Dai et al. 2008; Kathiravan and Raman 2010;
Xu et al. 2010; Senthil Kumaran et al. 2011). The ubiquity,
diversity and biology of the species of Phomopsis encourage
the need for evaluation of potential applications of these
fungi. A key argument in favor of studying taxonomy and
conserving biodiversity is that as yet undiscovered biodiversity will yield products of important and beneficial use for
humans. However, any link between undiscovered biodiversity and useful products is however, largely conjectural
(Smith et al. 2008).
Phomopsis as biocontrol agents
Biological control of weeds by plant pathogens has
gained acceptance as a practical, safe, environmentally
beneficial, weed management method applicable to
agroecosystems (Charudattan 2000). There has been
remarkable attention directed towards bioherbicides or
mycoherbicides (i.e. inundative use of fungal pathogens)
in advancing biocontrol strategies (Mortensen 1997;
Charudattan 2000; Trujillo 2005).
Some species of Phomopsis have been reported as
potential mycoherbicides to control invasive and destructive weeds due to their hemibiotrophic to necrotrophic life
mode, extensive sporulation and persistence in the environment (Rosskopf et al. 2000a, b).
The toxins and enzymes involved in physiological and
biochemical functions of hemibiotrophs and necrotrophs
are important targets for the studies in biocontrol and
molecular plant pathology and instrumental to design
rational strategies for disease control (van Kan 2006).
Knowledge of the pathogen life cycle also drives the
effective control of plant diseases (González-Fernández et
al. 2010).
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Fungal Diversity (2011) 50:189–225
Table 1 Phomopsis as biocontrol agents
Pathogen
Host/Target
Reference(s)
Phomopsis sp.
P. emicis Shivas
P. convolvulus Ormeno
P. amaranthicola Rosskopf, Charud., Shabana & Benny
P. cirsii Grove
Carthamus lanatus (Safron Thistle)
Emex australis
Convolvulus arvensis
Amaranthus sp.
Cirsium arvense
Ash et al. 2010
Shivas and Scott 1993
Ormeno-Nunez et al. 1988; Morin et al. 1989
Ortiz-Ribbing and Williams 2006
Leth et al. 2008
A greater use of mycoherbicides is important with the
movement towards organic farming and the restricted use of
herbicides (Ash 2010; Bailey et al. 2010). Examples of
potentially available Phomopsis in biocontrol of weeds are
listed in Table 1.
Research on biological control of weeds should target
the most urgent and problematic weeds where management
by conventional methods are not working and biocontrol
would have potentially significant benefits for users (Auld
and Morin 1995; Greaves et al. 1998; Charudattan 2001).
Therefore the discoveries on bioherbicidal Phomopsis
strains should follow the urgent needs. Therefore, pathogens on invasive plants should be reassessed and reported
as potential biocontrol agents. (Charudattan 2000; OrtizRibbing and Williams 2006). The wide host range of
species of Phomopsis, host specificity of some species and
mechanisms infection, pathogen persistence in the environment has been proven an utilizable tool in integrated weed
management systems (Ortiz-Ribbing and Williams 2006).
Secondary metabolites from Phomopsis
The discoveries of biologically active fungal metabolites
including new antibiotics, chemothereputic agents, and
agrochemicals have been the focus of the scientific
community worldwide. These fungal metabolites are
generally recognized as highly effective, possess low
toxicity, and have a minor environmental impact (Pearce
1997; Strobel and Daisy 2003; Smith et al. 2008; Xu et al.
2010). Pestalotiopsis, another coelomycetous genus, has
been shown to be highly creative with more than 130 novel
potentially medicinal metabolites discovered (Aly et al.
2010; Xu et al. 2010, Liu 2011).
Phomopsis is a similarly creative genus with several
important discoveries including exclusive and structurally
significant, physiologically active fungal metabolites
(Table 2).
Fungal endophytes have received increasing attention
by natural product chemists due to their diverse and
structurally unprecedented compounds which make them
interesting candidates for drug discovery (Strobel and
Daisy 2003; Zhigiang 2005; Huang et al. 2008; Mitchell et
al. 2010; Liu 2011). Endophytic Phomopsis strains have
gained attention in most cases involving metabolite
research. Because of the practical difficulty in Phomopsis
identification at the species level, most of these metabolite
producing strains are only recognized at generic level. The
utility of some of the novel metabolites in functional in
vitro systems are still unknown (Li et al. 2010a, b).
Taxonomy, phylogeny and species concepts of Phomopsis
There has been considerable attention given to the need for
revaluation of the taxonomy and phylogeny of Phomopsis
and its species; however it is currently well understood that
the conventional taxonomic characters no longer resolve
species of Phomopsis (Brayford 1990; Rehner and Uecker
1994). Recent approaches have used nucleic acid sequence
data to resolve species boundaries within the genus (Santos
et al. 2010; Diogo et al. 2010). However, a polyphasic
approach including morphology, molecular phylogeny,
pathogenicity and virulence of isolates biological species
should be adopted in future studies (Santos and Phillips
2009; Diogo et al. 2010) as recommended for other genera
such as Colletotrichum, Fusarium and Pencillium (Cai et al.
2009; Schroers et al. 2011; Hawksworth 2011).
In general, species concepts in fungi have evolved in
sequential phases due to the complexity of identification
of species (Shenoy et al. 2007); this includes the
morphological species concept, the ecological and physiological species concept, the biological species concept
and the evolutionary and phylogenetic species concept
(Moncalvo 2005). The species concepts of Phomopsis
have also been reviewed herein, based on similar phases
that would facilitate to resolve the problems of this genus.
Significance of hyperdiversity
Based on the current knowledge of Phomopsis, it is
challenging to identify a species isolated from a host for
which a species has not been described previously. This is
because many of known species have wide host range and
there are few characters that can differentiate them (Uecker
1988). Some species are thought to be host-specific; while
Source isolate
Host
Metabolites/enzymes
Known utilities of metabolites
Reference(s)
Endophytic
Phomopsis sp.
BCC 1323
Endophytic
Phomopsis sp.
BCC 9789
Endophytic
Phomopsis sp.
Endophytic
Phomopsis sp. B3
Phomopsis cassiae
Sousa da Câmara
Phomopsis oblonga
(Desm.) Traverso
Phomopsis
leptostromiformis
Endophytic
Phomopsis sp.
(#zsu-H76)
Phomopsis sp. A123
Tectona grandis
Phomopxanthone A,B
In vitro antimalarial, antitubercular
activities, cytotoxicity
Isaka et al. 2001
Musa acuminata
Six new oblongolides
Cytotoxicity
Bunyapaiboonsri et
al. 2010
Taxus cuspidate
Taxol
Anticancer activity
Bischofia Polycarpa
Laccase enzymes
Cassia spectabilis
Ulmus sp.
Ethyl 2,4-dihydroxy-5,6-dimethylbenzoate,
phomopsilactone
Several novel compounds
Biological Oxidation/microbial
industry
Antifungal activity, cytotoxity against
human cervical tumor cell line
Insecticidal activity
Senthil Kumaran
and Hur 2009
Dai et al. 2010
Lupinus sp.
Phomopsin
Excoecaria agallocha
Phomopsis-H76 A, B, C (novel)
Kandelia candel
Endophytic
Phomopsis sp.
Lz42
Phomopsis sp.
Phomopsis sp. KS37-2
Endophytic
Phomopsis sp.
Claydon et al. 1985
Yin et al. 1992,
Shivas et al. 1991
Yang et al. 2010
Five novel nonenolides, phomonol, phomotone,
phomophene
A new sesquiterpenoid, sterol and 5 known compounds
Not detected
Li et al. 2010a, b
Not detected
Lin et al. 2009
Mellein, nectriapyrone, 4-hydroxymellein, scytalone, tyrosol, clavatol, mevinic acid, mevalonolactone, Phomol
Benzophomopsin A (I)
Antimicrobial activity,
antinfammatory activity
Not detected
Redkoa et al. 2007,
Weber et al. 2005
Shino et al. 2009
Living bark of Cavendishia Generally,
conidiophores are hyaline, branched
pubescens
Twigs of Salix gracilostyla var.
melanostachys
Azadirachtae indica
Paspalitrems A 40, C 41
Tremorgenic activity
Bills et al. 1992
Phomopsichalasin
Antibacterial and antifungal activity
Tan and Zou 2001
Five ten-membered Lactones
Wu et al. 2008
Dicerandra frutescens: stem segment
Dicerandrol A,B,C
Antifungal activity against plant
pathogens
Antibiotic and cytotoxic activity
Hydnocarpus anthelminthicus
Mycoepoxydiene derivatives
Cytotoxicity
Prachya et al. 2007
Cortex stem of Vanilla albidia
Three new sesquiterpenes
Cytotoxicity against cancer cell lines,
Hemtasin et al. 2011
Erythrina crista-galli
Stem of cherry tree
Wagenaar and
Clardy 2001
195
Endophytic
Phomopsis sp.
Endophytic
Phomopsis sp.
Phomopsis
longicolla
(endophytic)
Endophytic
Phomopsis sp.
Phomopsis archeri
Silva et al. 2005
Antimitotic activity (inhibition of
microtubule assembly)
In vitro antibacterial activity and
cytotoxicity
Maytenus hookeri
Fungal Diversity (2011) 50:189–225
Table 2 Secondary metabolites/enzyme production by Phomopsis sp.
196
others are able to infect a wide range of hosts and therefore
caution is needed when concluding diversity in various
hosts (Mostert et al. 2001a; Crous 2005; Schilder et al.
2005; Santos and Phillips 2009; Diogo et al. 2010).
Phomopsis strains isolated from a single host may represent
more than one taxon (Rehner and Uecker 1994). There
have been recent phylogenetic studies on several species
complexes of Phomopsis associated with one particular
host. Fifteen species of Phomopsis have been recorded
from grape (Vitaceae) (Crous 2005; van Niekerk et al.
2005), which is remarkable. Other examples include wild
fennel (Foeniculum vulgare) which is host to several
species of Phomopsis (Santos and Phillips. 2009), four to
six species are known from soybean from different
geographic locations (Nevena et al. 1997; Zhang et al.
1998; Mengistu et al. 2007) and five species from
Aspalathus linearis in South Africa (van Rensburg et al.
2006). There have been several unidentified species
reported as endophytes in Tectona grandis, Magnolia
liliflora, Manglietia garrettii and Salix sp. (Horn et al.
1996; Promputtha et al. 2005; Murali et al. 2006; Udayanga
et al. 2011).
Species of Phomopsis associated with various hosts
(one host with many Phomopsis species) needs to be
resolved with a molecular phylogenetic approach as in
case of certain Phomopsis species complexes that have
been redefined (Santos and Phillips 2009). Phomopsis
species associated with conifers, Phomopsis species from
economic fruit trees and Phomopsis species associated
with economic crops are awaiting a revaluation by precise
identification of several different species records (Hahn
1930; Kanematsu et al. 1999). The tropical versus
temperate endophytic Phomopsis community, and species
associated with members of families Cucubitaceae,
Rosaseae, Magnoliaceae, Euphobaceae and Fabaceae
which are woody hosts in tropical and temperate regions
needed a revaluation with recollection of species associated with these trees (Holliday 1980; Chi et al 2007;
Murali et al. 2006).
Morpho species recognition of Phomopsis
Morphology has been the basis of nearly all fungal
taxonomic studies; therefore most previous compilations
and monographs are based on morphological taxonomy
(Hyde et al. 2010a, b). Similarly, early species treatments
of Phomopsis were based on morphology, culture characteristics and host association (Uecker 1988; Brayford
1990; Mostert et al. 2001a; Chi et al. 2007).
Phomopsis is characterized by ostiolate, black conidiomata (Fig. 2C) containing elongate, cylindrical phialides
(Fig. 2C) that may produce two types of hyaline, non
Fungal Diversity (2011) 50:189–225
septate conidia- namely alpha and beta (Rehner and Uecker
1994). In some species, however, there are intermediates
between these conidial types (Fig. 3). The alpha conidia are
aseptate, generally hyaline, fusiform and usually biguttulate, but sometimes lack of guttules or have more guttules
(Figs. 2A, 3A–I). The beta conidia are also aseptate and
hyaline, but are filiform, straight or more often hamate and
lack guttules (Figs. 2A, 3) (Sutton 1980). Generally,
conidiophores are hyaline, branched and occasionally they
are short and 1–2 septate (Fig. 2B). Frequently, they are
multiseptate and filiform with enteroblastic, monophiladic
conidiogenesis (Punithalingam 1985; Crisescu 2003).
A third type of conidia called gamma conidia have been
recorded (Rosskopf et al. 2000a, b; Cristescu 2007). These
conidia are hyaline, multiguttulate, fusiform to subcylindrical with an acute or rounded apex, while the base is
sometimes truncate (Fig. 3J) (Mostert et al. 2001a;
Punithalingam 1974; Rodeva et al. 2009). Those species
described, having a third type of spores are Phomopsis
hordei Punith. P. oryzae Punith., P. phyllanthi Punith., P.
amaranthicola Rosskopf, Charud., Shabana & Benny., P.
capsici (Magnaghi) Sacc., P. elaeidis Punith., P. eugeniae
Punith., P. viticola Sacc. and P. sedi Punith.
The Diaporthe sexual state is characterized by ascomata
which are usually immersed in the substrate, often
erumpent through a pseudostroma mostly surrounding the
ascomata and have more or less elongated perithecial necks
(Fig. 2D). The pseudostroma is distinct and often delimited
with dark lines (Wehmeyer 1933). Asci are unitunicate,
clavate to clavate cylindrical, loosening from the ascogenous cells at an early stage and lying free in ascoma (Fig.
2D). Ascospores are biseriate to uniseriate in the ascus,
fusoid, ellipsoid to cylindrical, straight, inequilateral or
curved, septate, hyaline and sometimes with appendages
(Wehmeyer 1933; Muntanola-Cvetković et al. 1981).
Several different methods have been employed to induce
anamorphic sporulation and teleomorphic structure formation
of Phomopsis isolates in the absence in general methods
(Onesirosan 1978; Brayford 1990; Kanematsu et al. 1999;
Rawnsley et al. 2004; Luo et al. 2004). However, because of
the overlap in conidial size between species it is no longer
possible to delimit species of Phomopsis based on morphology alone (Van der Aa et al. 1990; Webber and Gibbs 1984;
Brayford 1990; Rehner and Uecker 1994). In addition, some
of these characters, vary with cultural conditions and media
used, for example the zonation and pigmentation of aerial
mycelium may be influenced by light (Brayford 1990).
Kanematsu et al (2000) identified two major morphologically distinct groups on the basis of colour of the
colonies on PDA (Table 3). They further recognized the
same two basic types as W and G types further on basis of
virulence of Phomopsis from peach, Japanese pear and
apple in Japan where G type isolates are more virulent in
Fungal Diversity (2011) 50:189–225
197
Fig. 2 A Alpha and beta
Conidia of Phomopsis anacardii,
B Conidiopores of P. anacardii.
C Vertical section of stroma of P.
anacardii. D Ascus of the sexual
stage of P. helianthi, E
Ascospores of P. helianthi
(Diaporthe sexual state) F
Conodiophores with paraphyses
among conidiogenous cells of P.
longiparaphysata Scale bars: A,
B,D,F = 10 μm, C = 200 μm
E = 5 μm. References: A,B,C:
Revised and redrawn from
Punithalingam 1985, D
Muntanola-Cvetković et al. 1981
F Uecker and Kuo 1992
inoculation in the field than that of W type (Kanematsu et
al. 1999, 2007).
Sutton (1980) used the term paraphyses for sterile
hyphae in his descriptions for other genera of phialidic
coelomycetes. A few species of Phomopsis have been
reported to have paraphyses (Rehner and Uecker 1994).
Phomopsis javanica Uecker and Johnson (1991) was
distinguished from other taxa found on asparagus such as
P. asparagi (Sacc.) Grove, based on the occurrence of
paraphyses. Previous indications of such structures were
also in Phomopsis theae Petch and P. anacardii Early &
Punith (Punithalingam and Gibson 1972). A further
occurrence of long paraphyses has been reported for
Phomopsis longiparaphysata Uecker & Kuo, a taxon from
198
Fungal Diversity (2011) 50:189–225
Fig. 3 Comparison of anamorphic spore morphology of Phomopsis (A–C) Biguttulate alpha
conidia (D). Multiguttulate
alpha conidia (E–I). Eguttulate
alpha conidia (J). Gamma
conidia (K–M). Various types of
beta conidia (not in scale)
Revised and redrawn from:
Punithalingam et al. 1974,
Mostert et al. 2001a, b; Van
Niekerk et al. 2005
grapes in Taiwan (Fig. 2e) (Uecker and Kuo 1992). Such a
distinctive character is welcome in the study of a group
noted for a dearth of such characters (Uecker and Johnson
1991).
Fungal Diversity (2011) 50:189–225
199
Table 3 Designation of W and G types of Phomopsis
Type of
colony
Surface view
Reverse view
Sporulation
Virulence
W type
White, aerial hyphae, scatteredrelatively large stroma, irregular
pycnidial locules
A few aerial hyphae, white to grey and formed abundant
relatively small pycnidial stroma with irregular pycnidial
locules
Both alpha and
beta conidia on
PDA
Only alpha
conidia on PDA
Less
virulent
G type
Whitish and occasionally had
pale pink, brown and or grey
zones
Grey or brownish grey
More
virulent
Source: Kanematsu et al. 1999, 2000
Pathogenicity and virulence
The capacity of a fungal species to cause a disease (i.e.,
pathogenicity) and the degree of pathogenicity (i.e.,
virulence) have been used to differentiate pathogenic
species (Uddin and Stevenson 1997, 1998a, b; Schilder et
al. 2005). The need for comparative studies of pathogenic
Phomopsis species using morphology, and pathogenicity
has also been emphasized by Kanematsu et al. (1999).
Herein we discuss several incidents of pathogenicity testing
and cross inoculation experiments with arguments made for
and against them.
Pathogenicity testing of species of Phomopsis infecting
grapes revealed that different isolates of P. viticola cause
disease symptoms, but differed in virulence, estimated on
the size of lesions (Schilder et al. 2005). In the same study,
specialization of pathogens on specific plant tissues was
observed and one distinct taxon was distinguished based on
its severity of infection on grape fruits. Further characterization revealed that, the isolate, which differed in virulence, resembles a species originating from another host in
the vicinity of the vineyard. However the observations
based on virulence and pathogenicity were mostly of a
quantitative nature and thus it is difficult to assign any
species on these observations alone (Schilder et al. 2005).
Vidić (1991) studied the variability of virulence among
isolates of D. phaseolarum var. caulivora on three varieties
of soybean in Serbia but was unable to support or reject
their separation into different physiological races based on
severity of infection (Rehner and Uecker 1994). Uddin and
Stevenson (1998a, b) has been reported on pathogenic and
molecular characterization of three Phomopsis isolates from
peach, plum and Asian pear. They observed that there was
no significant difference between the length of cankers on
peach shoots inoculated with plum and Asian pear isolates,
and they were significantly smaller than those inoculated
with peach isolate. All three isolates differed in morphology
and ITS sequence data, although the phylogenetic affinity
between the pear and plum isolates was closer than the
peach isolate. Susceptibility of the apple, plum and pear to
the pathogen causing shoot blight on peach was also
confirmed, providing evidence of their capability to one
particular host.
A species of Diaporthe occurring on grapes in Portugal
was identified as D. perjuncta, which shows little resemblance to P. viticola, apart from its association with Vitis.
Although several species of Phomopsis infect grapevines
worldwide, it has been reported that Australian isolates of
Diaporthe australaficana (formally D. perjuncta) do not
cause Phomopsis cane and leaf spot disease in Australia
(Rawnsley et al. 2004). Pathogenicity testing suggested that
D. perjucta is less prone to be a pathogen and is more likely
to be an endophyte in Vitis. However, D. perjuncta was
recollected from Ulmus glabra in Germany, and distinguished from D. viticola by morphology and ITS based
phylogeny and the taxon has been established (van Niekerk
et al. 2005).
The wide host range of Phomopsis has great implications
for the management of diseases caused by different species as
alternative hosts might act as source of inocula which would
be a challenge in management of disease and quarantine.
Therefore, the assessments of virulence, pathogenicity and the
knowledge of disease cycles are equally important in future
concerns in plant pathology and taxonomy. It is important to
establish if a particular Phomopsis is host specific or not and
epitypification and performing Koch Postulates is important
in describing new species, while pathogenicity alone could
not contribute to the differentiation of species.
Chemotaxonomic markers, biochemistry and serology
In its broadest sense, chemotaxonomy is the use of
chemical diversity as a taxonomic tool, which refers to
the use of secondary metabolites in the classification of
filamentous fungi (Frisvad et al. 2008). In this section we
explore the use of chemotaxonomy as a tool to differentiate
Phomopsis species. A profile of secondary metabolites
consists of all the different compounds a fungus can
produce on a given substratum and includes toxins,
antibiotics and other different compounds. Chemotaxonomy
is regularly used in polyphasic approaches to genera such as
200
Aspergillus and Penicillium (Frisvad et al. 2008) and has
been suggested for use in Colletotrichum (Abang et al. 2009;
Cai et al. 2009). Although Phomopsis species have been
extensively screened in bioassays for metabolite production (Isaka et al. 2001; Weber et al. 2005; Yang et al.
2010) the utilization of chemotypes for species recognition
has been limited.
Phomodiol, Phomopsolide B and Phomopsichalasin were
recognized as potential chemotaxonomic markers in endophytic Phomopsis isolates from woody hosts (Horn et al
1994). Two of these secondary metabolites were evaluated as
potential chemotaxonomic markers for the endophytic
Phomopsis isolates from Salix sp. (Willow) and several
other hosts (Horn et al. 1995). Phomopsis isolates from
willows and non willow isolates were tested for the
production of these two chemicals in both malt and millet
media. Phomopsolide B was produced by all the isolates
from willow and one isolate derived from different woody
host. Phomodiol production however varied among all
isolates (Horn et al. 1996).
Shivas et al. (1991) demonstrated infraspecific variation
in Phomopsis leptostromiformis from Western Australia
using cultural and biochemical techniques. They recognized
two different varieties of Phomopsis leoptostromiformis
based on the observations from pectic estrase zymograms
and quantities of phomopsins A and C in assay conditions
provided. Phomopsins were analyzed in the extracts of
culture by high-performance liquid chromatography
(HPLC) (Shivas et al. 1991).
The antibodies derived from immunized rabbit serum for
powdered mycelium of freeze dried Phomopsis was successfully used to detect the fungus infected to the soybean seed.
Antiserum to freeze dried powdered mycelium of Phomopsis
longicolla was used in an indirect ELISA (Enzyme Linked
Immunosorbent assay) and a modified immunoblot assay for
seed born pathogen infection (Gleason et al. 1987). Possible
implications of detection of P. longicolla and its varieties
using the monoclonal antibodies were also discussed in order
to prevent the cross reactivity of antiserum in the above
mentioned methodology (Gleason et al. 1987). Metabolites,
mycotoxins and antibodies based diagnostic methods have
prompted as alternative quick, specific and sensitive attempts
in plant pathogen detection which surpass the traditional
inconclusive methods (Ward et al. 2004). The lack of
utilization of metabolite profiling and chemotaxonomic
approaches in Phomopsis is not surprising due to rapid
progress of molecular based identification.
Implications of antagonism
The degree to which the growth of the fungal cultures is
affected by the proximity of actinomycetes varied in
quantitative expression, depending on the species combi-
Fungal Diversity (2011) 50:189–225
nation used in co culture. This repressive physiological
action between two organisms (fungus and actinomycete)
inhibiting the fungal growth (i.e. antagonism) has used in
species recognition of Phomopsis.
Muntanola-Cvetković et al. (1990, 1992, 1996) reported
on the repressive effect of some actinomycetes on the growth
of Phomopsis isolates which could be relevant in distinguishing Phomopsis species. Fifty five asexual and sexual strains
of Phomopsis were analyzed for antagonism by five selected
Streptomyces species (Muntañola-Cvetkovic et al. 2000). The
responses of the fungi varied, but two major groups could be
distinguished. Group A encompassed isolates less affected
by actinomycetes and Group B comprised those exhibiting
high sensitivity in all experiments. Group A was typically
represented by Diaporthe arctii, Phomopsis longicolla and
the Phomopsis type 1 culture from Xanthium italicum,
whereas group B was typically represented by Phomopsis
helianthi and Phomopsis type 1 cultures from X. italicum and
isolates from Lactuca serriola. The results obtained underscore the differences between D. arctii and P. helianthi and
corroborate the value of the physiological aspects of
congeneric isolates in considering taxonomic problems in
Phomopsis (Muntañola-Cvetkovic et al. 2000). However the
contribution based on these experiments are minimum and
dependent therefore not recommended in initial stages of
species identification (Fig. 4).
DNA based alternative or comparative assays
DNA based comparative assays have proven to be useful in
phylogenetic studies therefore utilized to evaluate the genetic
diversity of Phomopsis especially when the DNA sequence
facilities are not applied in large scale (Zhang et al. 1997,
1998; Chi et al. 2007; Santos and Phillips 2009). These
methods are in partial agreement with phenotypic and
genotypic groups and some have been used in infraspecific
taxonomy (Vergara et al. 2005).
Restriction fragment length polymorphism (RFLP)
RFLP has been used to distinguish between Phomopsis and
other pathogens from soybean. PCR-RFLP patterns from
ITS amplicons using 20 different restriction enzymes and
was used in sequence analysis to distinguish P. longicolla
and D. phaseolorum isolates from other soybean fungal
pathogens (Zhang et al. 1997). The distinguishing patterns
of RFLP from ITS amplicons were observed for Phomopsis
isolates as compared to other associated pathogens using
the same restriction enzymes.
Zhang et al (1998) used ITS based phylogeny and RFLP
patterns of amplified products of ITS for the Phomopsis
isolates derived from soybean as molecular markers in
Fungal Diversity (2011) 50:189–225
201
Fig. 4 Repressive effect on P. helianthi by Streptomyces diastaticus
subsp. ardesiacus A CBS 592.81 (type of P. helianthi) Vs. CBS
100.56 (Streptomyces diastaticus subsp. ardesiacus) 2 weeks old coculture shows the increasing inhibition of the growth of P. helianthi by
forming an inhibition area in the middle of the culture (positive
results) B CBS 592.81 (control) P. helianthi isolates without
Streptomyces inoculation C CBS117499 (type of P. cuppatea) vs
Streptomyces diastaticus subsp. ardesiacus: without considerable
antagonistic reaction (negative results). *Methodology: MuntanolaCvetkovic et al. 2000
species detection. Restriction analysis of ITS by AluI, MseI,
HhaI, RsaI, and ScrFI was used to detect subgroups of species
of P. longicolla and Diaporthe phaseolorum. Extensive
genetic variability was observed in D. phaseolorum isolates
with the RFLP patterns.
PCR-RFLP based analysis was undertaken to delineate
the Diaporthe species from stone and pome fruits in south
Africa with special reference to infection by a ds RNA
mycovirus, Diaporthe ambigua RNA virus (DaRV) (Preisig
et al. 2000; Moleleki et al. 2002). RFLP patterns and
sequencing information were used to identify three different
Diaporthe species namely Diaporthe amugua, D. perjuncta
and an unidentified Phomopsis sp. The species infected by
the dsRNa virus was D. perjuncta and not D. ambigua
(Moleleki et al. 2002).
Species specific probes
Random amplified polymorphic DNA (RAPD)
Chen et al. (2002a, b) evaluated the applications of RAPD
and ITS sequence data on 34 Phomopsis isolates from
China. This study revealed that RAPD data nearly
coincides with morphological data and mostly with the
ITS sequence data.
Microsatellite primed PCR (MSP-PCR)
Microsatellite primed PCR profiles were generated for the
isolates of Phomopsis and Diaporthe (Santos and Phillips
2009; Diogo et al. 2010). Representative isolates from
meaningful groups at higher reproducibility levels were
selected for phylogenetic analysis. This method is important to assess when large number of isolates are present
from same or relative hosts and environment which avoids
the repetitive sequencing of the same isolates and recognizes the comparative genetic variability of isolates.
Species specificity is an important criterion for DNA-based
diagnosis. Melanson et al. (2002) has used taxon-specific
probes to detect Phomopsis sp. 1 and 2 from grapes. Their
investigation used specific markers for Phomopsis infecting
grapes to determine their origin in Australia. Zhang et al.
(1997) used Phomopsis specific primers (PhomI and Phom
II) for the amplification of 337 bp from the ITS region to
distinguish isolates of P. longicolla and D. phaseolorum
from other soybean pathogens. None of the amplified
products was observed in the DNA of seven other soybean
fungal pathogens or soybean plant genomic DNA.
Species specific detection of Diaporthe phaseolorum
and P. longicolla from soybean seeds was achieved using
high throughput techniques (Zhang et al. 1999). They
designed primer probe (Taq man) sets to detect P. longicolla
in the seeds of soybean with high sensitivity at 0.15 ng
(four copies) of plasmid DNA.
Current advances in gene sequencing and analysis will
result in many of the methods mentioned above being used
less frequently as they no longer provide significant results
as compared to modern techniques. However, alternative
and comparative assays are still employed in selection of
strains for sequencing, population studies, infraspecific
taxonomy, evolutionary studies and studies of genetic
diversity of fungi (Riccioni et al. 2008; Santos and Phillips.
2009; Diogo et al. 2010).
Molecular phylogenetic approach in the study
of Phomopsis
The current state of species of Phomopsis, effectively
means that a particular isolate be identified to species level
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Fungal Diversity (2011) 50:189–225
only if molecular techniques are employed (Crous 2005).
Classification of fungi based of DNA sequence data which
infer evolutionary relationships has been widely adopted
(Shenoy et al. 2007) and has successfully been used to
differentiate species in several important pathogenic genera
including Phomopsis (Santos and Phillips 2009; Diogo et
al. 2010; Cai et al. 2011). Although the DNA-based methods
provide convincing results, there are several challenges to
overcome to establish a more precise taxonomic frame for
the genus.
ITS rDNA sequences and morphology
There have been several studies using ITS sequence data
along with morphology to investigate species of Phomopsis. Rehner and Uecker (1994) examined 43 North
American and Caribbean strains of Phomopsis from a
diverse range of hosts by analysis of ITS1 and ITS2
sequence data. Three basic phylogenetic groups (A, B and
C) were identified and defined on basis of geographic
origin and the host association (Table 4).
They defined ITS sequence based phylogenetic groups
for the isolates obtained from Asia, Europe and North
America. They also noted that variation in ITS sequence
data may lead to the introduction of cryptic species of
Phomopsis and therefore further refinement of available
taxa was recommended. Groups of Phomopsis were further
interpreted with possible distinction on the basis of
geographical, morphological and host affiliation. The
problem with this study, however, was that no extype strain
of Phomopsis was used and the isolates were randomly
selected from various locations worldwide.
Murali et al. (2006) studied the foliar endophyte
assemblages from teak trees (Tectona grandis) in India
using ITS sequence data from 11 different Phomopsis
isolates (ten from teak and one from Cassia fistula). The
data were analyzed with more than 50 sequences downloaded from GenBank. The authors showed that the isolates
fell into two strongly supported groups. The study did not
describe any distinct species from teak, but supported
earlier studies concluding that Phomopsis from teak are not
host-specific, and that the species concepts in Phomopsis
need to be redefined.
Santos and Phillips (2009) successfully used ITS
sequence analysis combined with micromorphology to
resolve the complex of Phomopsis occurring in Foeniculum
vulgare (wild fennel) in Portugal. Four species were
distinguished. Diaporthe angelicae (Berk.) D.F. Farr &
Castl. was shown to be the most common pathogen of this
host, D. lusitanicae Phillips & Santos was newly described,
the teleomorph of Phomopsis theicola Curzi was revealed
to be distinct from Diaporthe theicola Curzi and described
as D. neotheicola Phillips & Santos.
Multilocus phylogenies of Phomopsis
The combined analysis of more than one gene provides higher
resolution than a single gene. For example, Van Rensberg et al.
(2006) used ITS and partial elongation factor 1 α (EF1α)
sequence data, plus morphological and cultural observations
to characterize species of Phomopsis associated with dieback
of Rooibos tea (Aspalathus linearis) in South Africa. The
combined sequence data supported the differentiation of the
same six species as identified by ITS phylogeny, but with a
higher level of confidence.
Farr et al. (2002a, b) also discussed the importance of
combining molecular and morphological characters in
species identification. Ambiguities in the alignment of ITS
sequence data across the genus Phomopsis was also noted
(Farr et al. 2002a, b). Large numbers of ambiguously
aligned regions may obscure the true relationships among
taxa and the parsimony analysis of ITS sequence data for
this group indicates that there is a large amount of
homoplasy across the entire genus (Farr et al. 2002a, b).
Therefore the number of branching orders with fewest
evolutionary events to explain contemporary sequences
(i.e.; the number of parsimonious trees) might be higher
than usual. Use of multiple sequence data using several
combined genes in phylogenetic analyses would be
needed as in Colletotrichum and other several complex
Table 4 Phylogenetic groups of Phomopsis isolates inferred based on ITS sequence data
Group identity
Host range and specific characters
Geographic range/origin of isolates
Group A : Subclade
A1
Group A : Subclade
A2
Group B
Variety of host genera
Eastern and Midwestern United States
Vaccinium sp.
United States (Massachusetts and
Michigan)
Southern temperate to tropical regions
Group C
Woody and herbaceous plants produce paraphyses among their conidiogenous
cells
Primarily on herbaceous plant hosts, including agricultural field crops and
some woody plants
Source: Rehner and Uecker 1994
Temperate to subtropical regions of
United States
Fungal Diversity (2011) 50:189–225
genera (Vergara et al. 2004; Cai et al. 2009; Crouch et al.
2009; Prihastuti et al. 2009; Aveskamp et al. 2010;
Phoulivong et al. 2010), to better resolve species relationships.
ITS, EF 1α partial sequence data and MAT phylogenies
of Phomopsis were compared without combining the genes
in phylogeny to establish correlation between biological
and phylogenetic species concepts (Santos et al. 2010). ITS
sequence data was shown to be highly variable within a
biological species of Phomopsis (as Diaporthe), while
partial sequences from the translation elongation factor 1α
were more reliable indicators of species limits. Nevertheless, ITS sequence data can be used for reliable identification of phylogenetic relationships as long as they are
interpreted with care. When compared to previously
reported data for other genera such as Colletotrichum (Du
et al. 2005), the ITS region in Phomopsis appears to be
evolving at much faster rates than EF1-α or even MAT
genes (Santos et al. 2010). Therefore a slowly evolving
gene region should be utilized in order to establish precise
species limits. Santos et al. (2010) has suggested that the
Ef1α derived sequences of Phomopsis and Diaporthe are
congruent with biological species clusters inferred by MAT
phylogenies. Finding a slowly evolving single copy gene
region with minimum infraspecific variability is still a
challenge for most fungal genera (Schmitt et al. 2009).
Incongruence of single gene phylogenies is thought to be
cause by various analytical and biological factors (Rokas et al.
2003a). The impact of those errors would be eliminated by
optimizing the conditions in change of the analytical
criterion such as elimination of outgroup in analysis to a
certain extent. Multigene gene phylogenies, would however,
be more robust providing valuable information for selection
of single genes to with less incongruence with true
polygenetic relationships (Rokas et al. 2003b).
There is an unprecedented need to use the multigene
phylogenetic relationships in order to eliminate the incongruence that would result using single gene analysis and to
establish meaningful evolutionary relationships.
Need for advancement in understanding Phomopsis
The need for of advancement in understanding of Phomopsis
is driven because (1) many sequences deposited in GenBank
are wrongly named because of lack of comparison with type
derived sequences (Cai et al. 2011), (2) many GenBank
sequences are named only to generic level, (3) there is a
advancing trend of research of biological species concepts
and infraspecific taxonomy, and (4) there is a lack of existing
type derived cultures and sequences. This situation should be
rectified in future studies of the genus. Isolates that represent
type species are needed. Publication of new species should
be amalgamated with type derived sequences and type
203
derived cultures should deposit in recognized culture
collections (Shenoy et al. 2010; Abd-Elsalam et al. 2010;
Hyde et al. 2010a, b). Species and infraspecific research
should be expanded and incorporate a polyphasic approach.
Type culture derived ITS phylogenetic tree
as a backbone for identification
Crouch et al (2009) and Cai et al (2009) have revealed a
high error rate and frequency of misidentification (86% and
>86% respectively for Colletotrichum graminicola complex and C.gloesporoides complex), based on ITS sequence
similarity comparison compared to type materials. It is
therefore essential to use ex-type strains in molecular
studies. Otherwise putatively named species from genera with
few distinguishing morphological characters used in phylogenetic studies will perpetuate the problem of wrongly named
taxa in GenBank (Cai et al. 2011; Hyde et al. 2011). Even
voucher or authentic strains should be treated with caution as
there is no way of guaranteeing these are identical to the type
of a species.
ITS sequence data derived from ex-type isolates of
Phomopsis were located based on an extensive literature
search and downloaded from GenBank (Table 5). We also
downloaded sequence data of authenticated or voucher
cultures of Phomopsis, accepting that these strains are less
reliable than extype cultures and should be epitypified. All
sequences were optimized manually to allow maximum
alignment and maximum sequence similarity with gaps
treated as missing data. The aligned dataset were analyzed
using PAUP* 4.0b10 (Swofford 2002). Ambiguously aligned
regions of the dataset were excluded from all analyses. A
heuristic search option with TBR branch swapping and
1,000 random sequence additions were used to infer trees.
Maxtrees were unlimited, branches of zero length were
collapsed and all multiple parsimonious trees were saved.
Trees were figured in Treeview (Page 1996). The first of 145
equally parsimonious trees obtained from the heuristic search
is presented herein and provides a backbone of ex-type
derived ITS sequences that can be used as a rough and quick
identification guide for species of Phomopsis (Fig. 5).
The extype and voucher derived sequence data used here
(46 taxa) are limited when compared to the large number of
species names (981 names) listed for Phomopsis and its
sexual Diaporthe state (828 names) (Index Fungorum
2011). Not all described species of Phomopsis have been
sequenced; it would be an impossible task considering the
short period we have used molecular data in fungal
taxonomy and the history of species descriptions in the
genus. The type derived ITS phylogenetic tree however,
provides the basis for Phomopsis identification which can be
improved and expanded on as more data becomes available.
204
Table 5 Species of Phomopsis/Diaporthe with available sequence data and location of type/epitype cultures and their sequenced genes if available
Taxa
Type/epitype strain
Culture/available sequence
derived from
Genes sequenced
References for sequences
ITS
Ef 1α
MAT1-1-1
MAT 1-2-1
Rosskopf et al. 2000a, b
Diogo et al. 2010
Chang et al. 2004
Chang et al. 2004
Chang et al. 2004
Chang et al. 2004
Udayanga et al. 2011
van Rensburg et al. 2006;
Santos et al. 2010
Farr et al. 2002a, b
Santos et al. 2010
Santos et al. 2010
Udayanga et al. 2011
Chang et al. 2004
Chang et al. 2004
Chang et al. 2004
Miric et al. 2004; Santos et al.
2010
x
Chang et al. 2005
ATCC 74226
CBS 126679b
n.e.
n.e.
n.e.
n.e
n.d.
CBS117499
Holotype
Ex-epitype
Voucher
Voucher
Voucher
Voucher
Holotype
Holotype
AF079776
GQ281791
AY618930
AY601920
AY622996
AY622993
JF957786
AY339322
x
x
x
x
x
x
x
AY339354
x
x
x
x
x
x
x
GQ250252
x
x
x
x
x
x
x
x
P. columnaris
P. cotoneastri
P. dauci
P. emicis
P. eucommicola
P. eucommii
P. glabrae
P.helianthi
CBS109873
CBS 439.82
CBS 315.49
BRIP 45089 a
n.e.
n.e.
n.e
CBS 592.81
Holotype
Isotype
Ex-epitype
Holotype
Voucher
Voucher
Voucher
Paratype
AF439625
FJ889450
FJ889451
JF957784
AY578071
AY601921
AY601918
AY705842
x
GQ250341
GQ250348
x
x
x
x
GQ250308
x
x
x
x
x
x
x
GQ250234
x
GQ250286
GQ250289
x
x
x
x
x
P. javanica
P. lagerstromiae
P. leptostromiformis var
occidentalis
P. liquidambari
P. longicolla
ATCC 24624
n.e.
Holotype
Voucher
x
AY622994
x
x
x
WAC 5364
Holotype
x
x
x
x
x
n.e.
ATCC 60325
Voucher
Holotype
AY601919
x
x
x
x
x
x
x
Chang et al. 2004
x
P.
P.
P.
P.
P.
P.
P.
P.
n.e.
n.e.
n.e
n.e.
CBS 161.64
n.e.
n.d.
CBS 296.67, ATCC 18585
Voucher
Holotype
Holotype
Holotype
Holotype
Holotype
Holotype
Holotype
AY601917
AY622995
EU012334
AY620820
FJ889452
AY620819
AF387817
AF439626
x
x
x
x
GQ250349
x
x
GQ250350
x
x
x
x
x
x
x
GQ250253
x
x
x
x
GQ250290
x
x
CBS 187.27
CBS 268.32
Holotype
Holotype
DQ286287
JF957785
DQ286261
x
x
x
x
x
Chang et al. 2004
Chang et al. 2004
Yuan et al. 2008
Chang et al. 2004
Santos et al. 2010
Chang et al. 2004
Mostert et al. 2001b
Farr et al. 2002a, b; Santos et
al. 2010
van Rensburg et al. 2006
Udayanga et al. 2011
loropetali
magnoliae
mauritina
micheliae
phoenicicola
phyllanthicola
saccharata
sclerotioides
P. theicola
P. tuberivora
Fungal Diversity (2011) 50:189–225
P. amaranthicola
P. amygdali
P. averrhoae
P. bougainvilleicola
P. camptothecae
P. chimoanthi
P. castaneae mollissimae
P. cuppatea
Taxa
Type/epitype strain
Culture/available sequence
derived from
Genes sequenced
References for sequences
ITS
Ef 1α
MAT1-1-1
MAT 1-2-1
P. vaccinii
P. viticola
CBS 160.32
CBS114016
Holotype
Epitype
AF317578
AF230751
GQ250326
GQ250351
GQ250244
GQ250254
x
x
P. vitimegaspora
CCRC 33533 **, ATCC
201952**/STE-U 2675*
ATCC 24097, CBS 495.72
Holotype**/ex epitype*
AF 230749*
x
x
x
Santos et al. 2010
Van Niekerk et al. 2005;
Santos et al. 2010
Van Niekerk et al. 2005
Isotype
FJ889444
GQ250298
x
GQ250261
Santos et al. 2010
CBS 114015
CBS 111592
Ex-epitype
Holotype
AF230767
AY196779
GQ250299
GQ250302
GQ250229
x
GQ250262
x
D. aspalthi
CBS 117169/STE-U 5428
Holotype
DQ286275
DQ286249
x
GQ250267
D.
D.
D.
D.
CBS
CBS
CBS
CBS
113487
162.33
145.26
123213,CBS 123212
Holotype
Holotype
Holotype
Holotype
AF230744
FJ889445
FJ889446
GQ250190
x
x
x
GQ250235
x
x
GQ250268
GQ250269
D. melonis
D. neotheicola
CBS 507.78
CBS 123209,CBS 123208
Isotype
Holotype
GQ250237
GQ250238
GQ250271
GQ250272
D. perjuncta
CBS109745
Ex-epitype
FJ889447
EU814480/
GQ250192
AY485785
x
GQ250307
GQ250309
GQ250311/
GQ250310
GQ250314
GQ250315/
GQ250316
GQ250323
Santos et al. 2010
Castlebury et al. 2003; Santos
et al. 2010
Van Rensburg et al. 2006;
Santos et al. 2010
Van Niekerk et al. 2005
Santos et al. 2010
Santos et al. 2010
Santos et al. 2010
GQ250242
x
D. stewarti
D. strumella var.
longispora
D. toxica
D. viburni
CBS 193.36
CBS 194.36
Holotype
Holotype
FJ889448
FJ889449
GQ250324
GQ250325
x
GQ250243
GQ250276
x
Santos et al. 2010
Santos and Phillips 2009;
Santos et al. 2010
Van niekerk et al. 2005; Santos
et al. 2010
Santos et al. 2010
Santos et al. 2010
CBS 53493
CBS 158.29
Holotype
Holotype
x
x
x
x
x
x
x
x
x
X
D. viticola
STE-U 5683, CBS113201
Ex-epitype
AY485750
GQ250327
x
x
van Niekerk et al. 2005;
Santos et al. 2010
Diaporthe
alleghaniensis
D. ambigua
D. angelicae
australafricana
crotalariae
hickoriae
lusitanicae
Fungal Diversity (2011) 50:189–225
Table 5 (continued)
n.e. culture not existing, n.d not deposited in public collections or available with author’s collection, CBS Centraalbureau voor Schimmelcultures, Netherlands, ATCC American type culture
collection, BRC Biological resource center, Institute of Microbiology, Beijing, China, BRIP Queensland Plant pathology herbarium/culture collection: Australia, WAC Western Australia culture
collection (as CCBD in publication), STE-U Stellenbosch University culture collection, South Africa, CCRC culture collection and research centre, Hsinchu, Taiwan
205
206
Sexual state, mating types and molecular basis
of mating experiments
A recent molecular based study on Phomopsis (Santos et al.
2010) focused mainly on the principles of biological
species recognition with the rational selection of mating
types by a genetic approach, therefore widening the
understanding of biological species concept in this genus.
Herein, we discuss the need for incorporation of biological
species concepts in future research on the genus.
Phomopsis comprises homothallic, heterothallic and asexual members and therefore biological species recognition is
important (Rossman et al. 2007; Kanematsu et al. 2007). In
heterothallic (self-sterile) species, sexual development
depends on mating between isolates of opposite mating types.
Homothallic (self-fertile) species isolates produce the sexual
stages without the need of a mating partner and therefore
mating types cannot be defined in these organisms. Purely
anamorphic organisms do not form any sexual stage although
the mating type genes can be amplified (Santos et al. 2010).
The identity of mating types of fungi is determined by
the gene content at the mating type/mating type like (MAT
or MTL) locus, which usually includes more than one open
reading frames (ORFs) and encode for transcription factors
that regulate the sexual identity (Butler 2010). Mating types
in the ascomycota are usually bipolar, which means that the
mating types are determined by two possible DNA sequences
at the mating type locus comprising unrelated and unique
sequences even though they are in the same locus (Coppin et
al. 1997). This lack of sequence similarity between the two
alternate mating types is a characteristic property previously
related to four model ascomycetes, ie. Neurospora crassa,
Podospora anserine, Cochliobolus heterostrophus and
Magnaporthe grisea (Coppin et al. 1997). The term
“idiomorph” have been used to denote unrelated sequences
although present in the same homologous locus, rather than
using the term alleles (Butler 2010; Coppin et al. 1997).
Kanematsu et al. (2007) revealed that the structure of
MAT loci of Diaporthe W and G types, is distinctive feature
bearing homologous genes in opposite mating type loci.
Other heterothallic filamentous ascomycetes have dissimilar
structures in opposite mating type loci. Thus researchers of
Diaporthe and Phomopsis, tend to use “mating types”
rather than “idiomorphs” (Santos et al. 2010).
There have been several attempts to apply the biological
species concepts in Phomopsis using conventional means.
Brayford (1990) identified two morphological types of
Phomopsis termed group one and two using isolates from
Ulmus species from the British Isles and Italy; the groups
also corresponded to two mating types. Cross mating
experiments confirmed that group one consisted of two
mating types and was thus self sterile, whereas group two
was self fertile. No cross fertilization was detected between
Fungal Diversity (2011) 50:189–225
the two groups. Linders et al. (1995) demonstrated that D.
adunca (Roberge ex Desm.) Niessl was heterothallic with
two mating types by cross fertilization and development of
the Diaporthe sexual stage the following spring.
Kanematsu et al. (2000) employed morphology and
molecular techniques to elucidate the diversity of Phomopsis isolates from fruit trees. In the mating test experiments
they recognized that the W-type isolates from fruit trees
were heterothallic and inter-fertile even between isolates
belonging to different monophyletic groups inferring the
phylogeny of rDNA ITS comparison. In the same experiment, the isolates of the G-type and P. amygdali collected in
Japan were cross fertile. They have also shown the cross
fertility between the isolates from different hosts in same
morphological type by cross mating tests.
As well as conventional mating experiments, molecular
based methods have been utilized in mating type diagnosis.
Kanematsu et al. (2007) stressed that it was important to
use mating type genes in evolutionary relationships in
Diaporthe and Phomopsis. They also stated that mating
type genes would ultimately resolve most of the problems
in species recognition. This study was based on previous
data on the sexually incompatible groups of Phomopsis
from fruit trees isolated from Japan (Kanematsu et al.
2000). The hypothesis is that the reproductive isolation
between Diaporthe W and G types might occur because of
the differences of the mating type loci. Kanematsu et al.
(2007) cloned and sequenced the mating type genes of both
reproductively isolated groups, and found that the mating
type loci are similar in structure in contrast to other
filamentous fungi. Structure and expression analysis of
mating type loci was reported related for Diaporthe W-type
and G-type by PCR based methods. Sequence information
was provided in GenBank with accession numbers for those
mating type genes as Diaporthe W-type (MAT1-1:
AB199324; MAT1-2:AB199325), Diaporthe G-type
(MAT1-1: AB199326; MAT1-2: AB199327) (Kanematsu et
al. 2007). These sequences were used to design suitable
genus specific primers for mating type genes of Diaporthe/
Phomopsis (Kanematsu et al. 2007; Santos et al. 2010).
Santos et al (2010) designed the primers for the mating
type diagnosis of Diaporthe and Phomopsis using the
alignments of the mating type genes of conserved regions
of Diaporthe Wand G types (Kanematsu et al. 2007). These
primers were successfully utilized for the amplification of
part of the α1 box from MAT1-1-1 gene and part of the
HMG (high mobility group) domain from MAT 1-2-1 gene.
Mating experiments were conducted to verify the molecular
diagnosis of mating types (Santos et al. 2010). The method
of utilization of MAT primers in the molecular diagnosis of
homothallic and heterothallic members, and the selection of
compatible mating pairs has drastically reduced the number
of crossings in teleomorph induction in vitro (Santos et al.
Fungal Diversity (2011) 50:189–225
207
Fig. 5 Phylogram generated
from the parsimony analysis
based on rDNA ITS sequence
data derived from type, epitype
and voucher specimens. Bootstrap support values >70% are
shown below or above the
branch and strict consensus
branches are thickened.
(*cultures derived from type
specimens, newly generated
sequences are in bold).
The tree is rooted with Valsa
mali. CI (consistency index) =
0.507, RI (retention index) =
0.744, RC (rescaled consistency
index) = 0.377, HI (homoplasy
index) = 0.493
AY339322 P. cuppatea*
FJ889448 D. stewartii*
FJ889447 D. melonis*
AY196779 D. angelicae*
94 FJ889451 P. dauci*
GQ250190 D. lusitanicae*
100 AY620820 P. micheliae*
AY622993 P. chimonanthi
AY622996 P. camptothecae
AF230767 D. ambigua*
71
AF439626 P. sclerotioides*
AF439625 P. columnaris*
JF957785 P. tuberivora*
FJ889449 D. strumella*
AY601918 P. glabrae
96
AB302250 D. kyushuensis*
98 AF230749 P. vitimegaspora*
AY705842 D. helianthi*
98 DQ226275 D. aspalathi*
FJ889445 D. crotalariae*
AF387817 P. saccharata*
FJ889452 P. phoenicicola*
AY620819 P. phyllanthicola*
AY601917 P. loropetali
AY601919 P. liquidambari
EU012334 P. mauritina*
AY618930 P. averrhoae
AY601920 P. bougainvillicola
91
AY601921 P. eucommii
AY622994 P. lagerstroemiae
GQ250192 D. neotheicola* 1
99
EU814480 D neotheicola*
81
DQ286287 P. theicola*
FJ889446 D. hickoriae*
AF230751 P. viticola*
AY485785 D. perjuncta*
FJ889450 P. cotoneastri*
AY622995 P. magnoliae*
JF957786 P. castanea mollisimae *
AF317578 P. vaccinii*
FJ889444 D. alleghaniensis*
AY578071 P. eucommicola
GQ281791 P. amygdali*
94
AY485750 D. viticola*
AF230744 D. australafricana*
JF957784 P. emicis*
GU174589 Valsa mali
96
100
1
2010). Homothallic species were used to induce the
teleomorph in vitro whereas heterothallic species were
tested in cross mating tests. The only requirement for
successful mating was co inoculation with opposite mating
types of the same species (Santos et al. 2010).
MAT genes however, influence the determination of sex
hence; they play a key role in population genetics and
evolution of fungi and therefore provide meaningful
justifications in evolutionary studies (Kronstad and Staben
1997). Molecular phylogenetic approach in Phomopsis
should therefore be meaningful with incorporation of ITS,
MAT, EF1α and other reliable gene sequence based
evidence to overcome different problems in taxonomic
conclusions (Santos et al. 2010).
Infraspecific taxonomy
Infraspecific taxonomy considers taxa below the rank of
species according to the International Code of Botanical
208
Nomenclature-Vienna code, which includes subspecies,
variety and forma (McNeill and Turland 2005). Plant
pathologists use the categories of forma specialis and
pathotypes although they are not formal taxonomic ranks
(Cannon et al. 2000; Cai et al. 2009).
Phenotypic and genotypic characters can be used in
infraspecific taxonomy including pathogenicity, virulence,
biochemistry, physiology and gene sequence data. Infraspecific variation of phylogenetically utilizable genes is a
parameter for the selection of possible barcoding regions
for a particular genus of fungi (Herbert et al. 2003; Zhao et
al. 2011).
There have been several infraspecific taxonomic investigations on important Phomopsis plant pathogens which
cause significant losses to economically important crops.
This includes pathogens of sunflower (i.e. Phomopsis
helianthi), the complex of Phomopsis pathogens on
soybean (P. sojae, P. longicolla), and P. viticola and other
species that causes the diseases of grapes (Merrin et al.
1995a, b; Zhang et al 1997; Rekab et al. 2004; Viguié et al.
1999; Vergara et al. 2005).
Whether infraspecific ranks should be used for species
of Phomopsis is as yet undetermined and presently it
would be wise to avoid such usage until molecular data
can validate such ranking. Therefore the infraspecific
rankings are mostly avoided in the section of current
names. Infraspecific studies on common Phomopsis
pathogens are needed in future studies in order to
recognize distinct biotypes. Sequence based infraspecific
evaluations of phylogenetically utilizable genes may result
from future barcoding initiatives for Phomopsis.
Fungal Diversity (2011) 50:189–225
cation of cryptic species, but this is hampered by the lack of
type cultures (Cai et al. 2011; Hyde et al. 2010a, b, 2011).
DNA sequence data and living cultures significantly enhances the value of type material and the published species
description and thus every effort should be made to generate
and deposit such resources in public collections (Seifert and
Rossman 2010; Hyde et al. 2010a, b). Changes in the
botanical code may be needed to encourage this. In the
parsimony analysis using 42 ITS sequences named as
Diaporthe helianthi in GenBank numerous entries had
considerable evolutionary divergence from the type derived
sequence (Cai et al. 2011). This work shows the need for
comparison with type material and type sequence data in
phylogenetic studies of Phomopsis and its sexual Diaporthe
state in order to avoid the possible misidentification.
Phomopsis amygdali, the causal agent of twig canker
and blight of almonds was recently epitypified in a survey
of the pathogens in Portugal (Diogo et al. 2010). Although
an epitype should be derived from the same locality and
host as the type (Hyde and Zhang. 2008), the justification
for epitypifying P. amygdali was based on morphological
and ITS similarity of isolates from Italy, Portugal and
Spain. The specimens had been described from Prunus
dulcis (CBS-H 20420) and CBS 126679b was recognized
as ex-epitype culture (Diogo et al. 2010). This is the only
recent case of epitypification of a species of Phomopsis that
is an important phytopathogen.
There is an unprecedented need for mycologists to return
to the field, recollect species re-typify taxa with living
cultures and fully characterize the taxa in Phomopsis which
has a large number of species names mostly without DNA
sequence data or type cultures (Hyde et al. 2010a, b).
Type cultures, epitypification and novel species
Potential resource for future research initiatives
The study of type derived cultures and specimens are
fundamental to future studies on the taxonomic studies.
Some important type derived cultures has been lost due
to poor storage facilities. For example, many of the type
cultures for the species described from southern China
(Chi et al. 2007) are no longer viable or are lost (Pers.
comm. Prof. Zide Jiang). It is paramount that efforts are
made to preserve these important cultures (Abd-Elsalam et
al. 2010). If cultures are maintained in the regional
collections with limited resources, they should also be
deposited in international collections such as CBS and
ATCC. It is necessary to distribute holotypes, isotypes and
extype specimens and cultures in several herbaria and
culture collections, and deposit the type derived sequences
in public databases (Ozerskaya et al. 2010; Abd-Elsalam et
al. 2010).
There is an urgent need for re-inventory of plant pathogens
which as resulted from rapid progress in molecular identifi-
Fungal genomics and proteomics, genetic transformation,
gene knockout strategies and different molecular biological
applications have revolutionized the studies of fungal
biology in recent decades (Lorang et al. 2001; Birren et
al. 2002; An et al. 2010; González-Fernández et al. 2010;
Kano et al. 2011). The use of Phomopsis species for various
applications including biocontrol, adaptive responses of
endophytes and hosts, studies on host pathogen interactions, model systems for studying fungal pathogenicity,
mycotoxins and fungal metabolite research should be
significant other than its ubiquity as a pathogen (Anco et
al. 2009; Nevena et al. 1997; Hyde et al. 2011; Dai et al.
2010).
Initiatives have investigated species of Phomopsis as a
tool of studying fungal pathogenesis and Phomopsis
viticola, a pathogen on grapes has been transformed by
several marker genes (Guido et al. 2003; Anco et al. 2009).
Fungal Diversity (2011) 50:189–225
In one study, Phomopsis viticola was transformed by GFP
(green fluorescent protein) using protoplast mediated
transformation and penetration and invasion of the host by
the fungus studied by fluorescent microscopy. Transformations yielded mitotically stable strains without any change
in virulence on grape internodes and leaves in comparison
to the wild type. The transformed P. viticola strains were
considered to be a critical tool for elucidating fungal
penetration of host plants, invasive growth and the nature
of its host association and to explore the unknown
physiological function of beta conidia. The study speculated on the potential use of Phomopsis as a model organism
to study the molecular mechanisms related to pathogenesis
(Anco et al. 2009).
The endophytic Phomopsis strain B3 isolated from
Bischofia polycarpa (Chinese bishopwood) is thought to
have a symbiotic relationship with rice, peking spurge
(Euphorbia pekinensis) and peanut, stimulating growth and
acting as a pathogenicide (Dai et al. 2006; Yuan et al. 2007).
The fungus can colonize rice plants from inoculated
mycelium available in the soil (Dai et al. 2010). The
possible mechanisms of plant colonization by this strain
were examined. The ability to produce laccase enzymes and
form cavities in the surface of straw was observed by
enzyme assays and microscopy. It was suggested that the
endophyte can produce enzymes with entry points at the
surface of plant; in Phomopsis strain B3 the dominating
enzyme was laccase (Dai et al. 2010). This initial study
holds promise for future studies on horizontal transmission
of endophytes into living plants which may be important in
development of pathogen resistant crops.
Phylogenetic and evolutionary genomic research has
been a focal interest since this will resolve a wide range
of biological problems (An et al. 2010). Rapid advancement in the genomics of plant pathogenic fungi will speed
up understanding of plant pathogens in many areas
including host range and specificity, pathogenicity factors,
epidemiology, fungicide resistance, control and evolution
(An et al. 2010). Despite the importance as a pathogen on
crops and the fascinating biology of the genus, species of
Phomopsis have not yet been used in fungal genomics and
proteomics research. Phomopsis is potentially important as
a model genus for the studies of biology, pathology,
reproduction, genetics and evolution of coelomycetous
and therefore should be used as a resource organism for
future research.
209
Rehner and Uecker (1994) implied that at least 60 species
of Phomopsis are plant pathogens, but they did not list
them. Sutton (1980) stated that 400 taxa have been
described in Phomopsis, but there has been no modern
revisionary treatment of the genus. In this review, we have
provided an account of commonly used names of phytopathogens. These names have been compiled with emphasis on the
frequencies of recent plant disease reports or taxonomic
literature. In this regard we scanned the USDA database,
where 225 Phomopsis names are cited (http://nt.ars-grin.gov/
fungaldatabases/nomen/new_frameNomenclatureReport.
cfm), the NIAS database of plant diseases in Japan (http://
www.gene.affrc.go.jp/databases-micro_pl_diseases_en.php),
list of plant diseases annotated with host (http://en.wikipedia.
org/wiki/Lists_of_plant_diseases), database of New Zealand
fungi (http://nzfungi.landcareresearch.co.nz/html/mycology.
asp) and widely prevalent fungi of United States (http://
www.prevalentfungi.org/index.html). In addition, we examined various published plant disease lists for American
Samoa (Brooks 2004), Hawaii (Raabe et al. 1981), Nigeria
(Umechuruba and Biol 1997), Sri Lanka (Coomaraswamy
1979), Thailand (Department of Agriculture 1994), and
some books such as world list of Phomopsis with notes on
nomenclature (Uecker 1988), Flora Fungorum Sinicorum (in
Chinese) (2007), Higher fungi in tropical China (Zhuang
2001) and Fungus diseases of tropical crops (Holliday 1980)
for the names of phytopathogenic Phomopsis spp. The
compilation given is an initiation of reinventory of large
number of names existing in given databases.
The names of species of Phomopsis are given alphabetically in this section, with notes on first record of species,
author and publication details. Synonyms are not given as
these can be searched in Index Fungorum. We recommend
fresh collections be made and used as epitype specimens of
the important phytopathogenic taxa and deposition of
reliable molecular data in public databases for reliable
identification (Hyde et al. 2010a, b).
The following details are included for each species.
&
&
&
&
Names of common phytopathogens in current use
This review uses Index Fungorum in the starting point of
evaluation of name records where 981 names are cited as
epithets of Phomopsis (accessed on 20th December 2010).
Hosts and diseases are given with known distribution.
Teleomorph names are given where known. Four teleomorphic names are used as current name due to their
frequent use in the phytopathology literature, but there
will need revising in future studies
Notes are given on the species including important
taxonomic information, significance of host and disease,
economic value that encourage the epitypification
Several important references are cited in chronological
order for host and distribution data at the end each
note
Phomopsis amaranthicola Rosskopf, Charud., Shabana
& Benny, Mycologia : 117 (2000)
210
Disease and host: Stem and leaf blight of Amaranthus sp.
Distribution: USA (Florida)
Notes: Leaf lesions, expand, coalesce, and develop to the
leaf petiole, causing premature leaf abscission (Rosskopf et al.
2000a, b). The presence of a third type of conidia (gamma
conidia) was considered as a unique feature for the
identification of this species. This species differs from P.
amaranthi Ubriszy & Vörös (Ubriszy and Vörös 1966), a
Hungarian isolate from dead stalks of Amaranthus
retriflexus, in conidial size and specifically the presence
of gamma conidia. This pathogen has been developed as
an effective biological mycoherbicide, which has been
patented (US patent 5,510,316). The patent was granted in
1996 for isolate ATCC 74226, deposited as an undescribed
Phomopsis isolate with a wide range of mycoherbicidal
activity. The new species, based on this culture, was
introduced later in 2000. The report of patent describes
that this novel isolate of Phomopsis is effective against
different pigweed biotypes from USA and other regions of
the world (Charudattan et al. 1996). Three different
Phomopsis isolates had been previously granted US
patents, but none had proved effective against pigweed
(Charudattan et al. 1996).
References: Charudattan et al. 1996; Inacio et al. 1999;
Rosskopf et al. 2000a, b
Phomopsis alnea Höhn., Sber. Akad. Wiss. Wien,
Math.-naturw. Kl., Abt. 1 115: 681 [33 of repr.] (1906)
Teleomorph: Diaporthe alnea Fuckel
Disease and host: Dieback of alder Alnus glutinosa, A.
incana (gray alder)
Distribution: Europe (Denmark, France, Germany),
Russia, USA (Kentucky)
Notes: P. alnea has essentially been considered, together
with other bark-attacking agents, as a contributing saprobe
which further degrades the stems and branches of alder
trees already weakened by other pathogens and environmental stress (Moricca 2002).
References: Munk 1957; Oak and Dorset 1983; Moricca
2002; Mel’nik et al. 2008
Phomopsis amygdali (Delacr.) J.J. Tuset & M.T. Portilla,
Can. J. Bot. 67: 1280 (1989)
Disease and host: Twig canker, withering branches,
and blight of Prunus dulcis (almonds) and P. persica
(peach), on living twigs, branches, leaves and flowers of P.
amygdalus (bitter almond) and on living twigs of Persea
americanae (avocado), Prunus salicina (plum), Vitis
vinifera (grape)
Distribution: Brazil, Canada, China, Greece, Italy,
Portugal, Spain, South Africa, USA
Notes: P. amygdali infects the trees through leaf scars in
autumn and through buds, bud scale scars, blossoms, and
fruit scars in spring, causing serious losses in almond and
peach cultivation worldwide. Examination of the morpho-
Fungal Diversity (2011) 50:189–225
logical, cultural and molecular characteristics of USA
strains of Phomopsis showed that P. amygdali on almond
in Europe is the same as the fungus found on peach in the
USA, but different from the strains from peach and Asian
pear (Farr et al. 1999).
References: Tuset and Portilla 1989; Mostert et al.
2001a; Chi et al. 2007; Rhouma et al. 2008; Diogo et al.
2010
Phomopsis anacardii Early & Punith., Trans. Br. mycol.
Soc. 59: 345 (1972)
Disease, host: Dieback, inflorescence blight, dying of
shoots, leaf spots of cashew nuts (Anacardium occidentale)
(Anacardaceae)
Distribution: Tropical regions, Kenya Brazil, India,
Myanmar
References: Punithalingam 1985; Gurgel et al. 2000
Phomopsis archeri B. Sutton, Coelomycetes: 571
(1980)
Host and distribution: Pittosporium tenufolium
Distribution: China, Hong Kong, UK, Uruguay, USA
(California)
Notes: Sutton (1980) provided the specific name for a
homonym (P. pittospori Archer, 1973). Compared to the
original description, Sutton (1980) gave somewhat shorter
measurements for both alpha and beta conidia. P. pittospori
(Cooke & Harkn.) Grove, 1919 described from California,
has narrower alpha conidia.
Reference: Sutton 1980
Phomopsis asparagi (Sacc.) Grove, British Stem- and
Leaf-Fungi (Coelomycetes) 1: 169 (1935)
Disease and host: Stem blight of Asparagus officinalis,
defoliation of fern and spears
Distribution: Australia, China, Greece, Italy, Taiwan,
New Zealand, USA
Notes: Bausa Alcalde (1952) described a second species
from Asparagus, Phomopsis asparagicola Bausa Alcalde
on branches of Asparagus plumosus with the justification
of morphological dissimilarity.
References: Reifschneider and Lopes 1982; Sherf and
Macnab 1986; Davis 2001; Elena 2006; Reclame 2010
Phomopsis arnoldiae B. Sutton, Coelomycetes: 571
(1980)
Disease and host: Stem canker and dieback of Elaeagnus
angustifolia (Russian olive) Eucalyptus globulus, E. grandis,
Phoenix hanceana and Juglans nigra
Distribution: Canada (Ontario), Hong Kong, Italy, north
eastern United States, Uruguay
Notes: Sutton (1980) provided this specific name (P.
arnoldiae) for P. elaeagni Carter & Sacamano, which was a
homonym of P. elaeagni Sacc. This name exists as a
competing homonym to P. arnoldiae.
References: Green 1977; Maffel and Morton 1983;
Bettucci and Alonso 1997; Lu et al. 2000
Fungal Diversity (2011) 50:189–225
Phomopsis azadirachtae Sateesh, Shank. Bhat &
Devaki, Mycotaxon 65: 517 (1997)
Disease and host: Twig dieback of Azadirachtae indica
(neem)
Distribution: India (Karnataka, Tamilnadu)
Notes: This taxon was introduced as a new species from
Azadirachtae indica and considered different from Phomopsis abdita Sacc. from Melia azedarach (Meliaceae) by
morphological comparison and cross inoculation tests
(Sutton 1980; Sateesh et al. 1997). Molecular detection
of Phomopsis azadirachtae has been assessed by amplification of 5.8S rDNAwith genus specific primers from isolates
from the type location, and several other locations in India
(Nagendra Prasad et al. 2006; Girish and Bhat 2008).
Sequences are not available in GenBank from type material
and culture collection numbers are not provided in the
publications.
This species has been drawn considerable attention for
studying epidemiology and management of the disease,
phytotoxicity, crude toxin extraction and biocontrol by
microbial antagonism (Girish and Bhat 2008; Girish et al.
2009; Nagendra Prasad et al. 2010).
References: Sateesh et al. 1997; Fathima et al. 2004;
Girish 2007
Phomopsis brachyceras Grove, British Stem- and LeafFungi (Coelomycetes) 1: 196 (1935)
Host and disease: On dead twigs and stems of Ligustrum
vulgare (wild privet, common privet, European privet: a
garden ornamental), Jasminum mesnyi
Distribution: China, Romania, UK (Scotland)
Notes: Phomopsis ligustri-vulgaris Petrak is also associated with genus Ligustrum, only the dimensions of α
conidia are given and differ from those of P. brachyceras.
These species should be recollected to clarify the occurrence of different species on one host.
References: Cristescu 2003; Chi et al. 2007
Phomopsis capsici (Magnaghi) Sacc., Nuovo Giorn.
Bot. Ital., N.S. 23(2): 209 (1916)
Teleomorph: Diaporthe capsici Punith.
Disease and host: Dieback and leathery fruit rot of
various Capsicum spp.
Distribution: Australia, Fiji, Greece, India, Mexico,
Philippines, Puerto Rico
Notes: Tucker (1935) identified Diaporthe phaseolorum
(Cooke & Ellis) Sacc. from pepper fruits and stated that
Phomopsis capsici and Phoma capsici forma caulicola
should probably be included as synonyms for Diaporthe
phaseolarum. The name P. capsici has been used in recent
plant disease reports (Rodeva et al. 2009).
References: Punithalingam 1981; Rodeva et al. 2009
Phomopsis castanea (Sacc.) Petr., Annls mycol. 19: 207
(1921)
Teleomorph: Diaporthe castanea (Sacc.)
211
Disease and host: Associated with nut rot disease and
also endophytic in Castanea sp. (chestnuts)
Distribution: Australia, China, India, New Zealand
Notes: This pathogen was previously thought to be the
major causative agent of chestnut rot, a well known postharvest disease of chestnuts in Australia and New Zealand
(Washington et al. 2006). However, recently the chestnut rot
pathogen was reclassified informally as Gnomonia pascoe
Smith & Ogilvy (Smith and Ogilvy 2008).
However P. castanea is still recognized as a minor
pathogen in the southern hemisphere and a major pathogen
in the northern hemisphere on chestnuts. It reduces storage
life, limits export and market potential and is a potential
producer of the mycotoxin “phomopsin”, which could be a
health problem of chestnut consumers (Osmonalieva et al.
2001). Phomopsis castanea is frequently isolated from
apparently healthy nuts; hence it could occur endophytically either associated with kernal tissues or the shell
(Washington et al. 1997).
Reference: Smith and Ogilvy 2008
Phomopsis castaneae-mollissimae (Jiang Shu-Xia and
Ma Hong-Bing) Mycosystema 29: 467–471 (2010)
Disease, host and distribution: Leaf spot diseases of
Castanea mollissima (Chinese chestnuts).
Distribution: China (Shandong Province).
Notes: Infected leaves produce small spots, turn brown
and finally drop. The taxon was identified as distinct from
previously recorded species from chestnuts and was,
therefore, described as new.
Reference: Jiang and Ma 2010
Phomopsis cinerescens (Sacc.) Traverso, Fl. ital. crypt.
Pyrenomycetae 2(1): 278 (1906)
Teleomorph: Diaporthe cinerascens Sacc.
Disease and host: Cankers and diebacks of Ficus spp.,
including Phomopsis canker on weeping fig (F. bejamina),
twig dieback of F. benjamina and infection from pruning
wounds of Ficus trees
Distribution: Canada (Alberta, Newfoundland), in several
other geographical locations of the world.
Notes: The taxon requires attention since Ficus is an
important exotic garden ornamental plant across the USA
and Canada as well as in tropics.
References: Hampson 1981; Anderson and Hartman
1983; Benschop et al. 1984
Phomopsis citri H.S. Fawc., Phytopathology 2(3): 109
(1912)
Teleomorph : Diaporthe citri Wolf.
Disease and host: Associated with stem end rot and
melanose of Citrus fruits, Fortunella sp., Mangifera indica
and Citrus trifoliata (trifoliate orange), fruits and twigs of
Citrus aurantium, C. decumana, C. nobilis
Distribution: USA (Florida), China and other Citrus
growing places of the world
212
Notes: P. citri is a serious pathogen of Citrus causing
severe blemishing of fruit that reduces its value for the fresh
market. The fungus is a weak parasite on the host and can
be isolated and recovered only after short period of
infection (Mondal et al. 2007).
References: Punithalingam and Holliday 1975; McKenzie
1992; Whiteside 1993; Nelson 2008; Farr and Rossman
2011
Phomopsis columnaris D.F. Farr & Castl., Mycol. Res.
106(6): 747 (2002)
Disease and host: Twig dieback on stems of Vaccinium
vitis-idaea (lingonberry)
Distribution: USA (Oregon)
Notes: This taxon is distinguished from other species of
Phomopsis by the distinctive conidiophores that consist of
vertically aligned cells lining the base and sides of the
conidiomata (Farr et al. 2002a, b). Two other species have
been associated with dieback of Vacciniun spp. in the USA,
Canada and Europe namely P. vaccinii Shear from blueberry
and cranberry (Farr et al. 2002a) and P. myrtilli Petrak from
bilberry and whortleberry in Austria and the Czech
Republic.
References: Farr et al. 2002a
Phomopsis cucurbitae McKeen, Can. J. Bot. 35: 46
(1957)
Disease and host: Black rot disease of green house
cucumbers (Cucumis sativus), Citrullus vulgaris, Cucumis
melo var. cantalupensis, Luffa acutangula, L. aegyptiaca,
Cucurbita pepo
Distribution: The distribution is cosmopolitan.
References: McKeen 1957; Punithalingam et al. 1975;
Ohsawa and Kobayashi 1989
Phomopsis cuppatea E. Jansen, Lampr. & Crous, in
Janse van Rensburg, Lamprecht, Groenewald, Castlebury &
Crous, Stud. Mycol. 55: 72 (2006)
Disease and host: Die back of Aspalathus linearis
(Rooibos)
Distribution: South Africa (Western Cape Province)
Notes: The taxon is named after the primary use of the
host substrate, which is used for Rooibos tea (van Rensburg
et al. 2006). This pathogen was shown to be slightly
virulent on Rooibos by pathogenicity testing. The causative
agent of dieback of Rooibos was previously thought be D.
phaseolorum Cooke and Ellis (Sacc.), but recent studies
have shown that several different species are associated
with this host including P. cuppatea Jansen and Crous (van
Rensburg et al. 2006).
Reference: van Rensburg et al. 2006
Phomopsis diachenii Sacc., Annls mycol. 13(2): 118
(1915)
Disease and host: Associated with stems and dried seeds
of Pastinaca sativa, umbel browning and stem necrosis of
Caram carvi (caraway, meridian fennel)
Fungal Diversity (2011) 50:189–225
Distribution: Bulgaria, Czech Republic, Germany,
Lithuania, Poland
Notes: Fennels (Apiaceae) are widely known as hosts for
various Phomopsis/Diaporthe species such as Phomopsis
foeniculi Du Manoir & Vegh. on fennels of Italy, France and
Germany, Diaporthe angelicae (Berk.) Farr & Castl., D.
lusitanicae Phillips & Santos., P. theicola Curzi and D.
neotheicola Phillips & Santos. in Portugal (Kusterer et al.
2002; Santos and Phillips 2009). Phomopsis diachenii has
been a useful test organism in the study of the biotic activity of
caraway with other associated fungi (Machowicz-Stefaniak
2009).
References: Saccardo 1915; Sutton 1980; Rodeva and
Gabler 2004; Machowicz-Stefaniak 2009
Phomopsis diospyri (Sacc.) Traverso & Spessa, La Flora
micologica del portogallo, Bol. Soc. Brot. 25: 26–187(123)
(1910)
Disease and host: Twig dieback and shoot blight of
Diospyros sp. (persimmon), blight of branches of D. lotus,
D. virginiana and D. kaki
Distribution: China, Germany, Greece, USA (California,
South Carolina), Italy, Ukraine
References: Zhuang 2001; Chen et al. 2002a, b;
Cristescu et al. 2003; Thomidis et al. 2009
Phomopsis emicis R.G. Shivas, Mycol. Res. 96: 75
(1992)
Disease and host: Stem blight of Emex australis
Distribution: Australia (Western Australia) and South
Africa
Notes: Several pathogens and pests have been assessed
for potential application as biocontrol agent against the
weed, Emex australis (Morris 1984). The stem blight
pathogen, P. emicis, and the weevil, Perapion antiquum,
had been recorded as two potential biological control agents
for the annual weed E. australis in Western Australia with
their potential applications (Shivas and Scott 1993). P.
emicis was described on the basis of its distinctive
morphological and cultural characteristics as well as the
distinctive host (Shivas 1992).
References: Shivas 1992; Shivas and Scott 1993; Crous
et al. 2000
Phomopsis helianthi Munt.-Cvetk., Mihaljč. & M.
Petrov, Nova Hedwigia 34: 433 (1981)
Teleomorph: Diaporthe helianthi Munt.-Cvetk
Disease and host: Stem canker of Helianthus annus
(sunflower), from Xanthium italicum (Italian cockleburr),
on grapevines. The disease is also known as grey spot
disease of sunflower
Distribution: Australia, Eastern Croatia, Europe, South
Africa, USA.
Notes: This taxon was first recorded in 1980 in former
Yugoslavia (Serbia). Cotyledon and capitulum infections
have been observed in 1987 and 1992, respectively (Says-
Fungal Diversity (2011) 50:189–225
Lesage et al. 2002). Wide distribution and high genetic
variability of the pathogen lead to evolution of new
strains that could be more aggressive, causing large
yield loss and resistance to control strategies (Pecchia et
al. 2004; Rekab et al. 2004). More studies on infraspecific
phylogenies and investigations on genetic variability in
other sunflower growing areas of the world are strongly
recommended.
References: Jurković et al. 2007; Nikandrow et al. 1990;
Carriere and Petrov 1990
Phomopsis heveae (Petch) Boedijn, Rec. Trav. bot.
Néerl. 26: 423 (1929)
Disease and host: Dieback of young tissue of 4 month
old seedlings of unthrifty plants of Hevea brasiliensis
Distribution: Brazil, China, India, Indonesia, Malaysia,
Sri Lanka, Thailand
Notes: This tropical pathogen causes dieback of young
seedlings and is a severe problem in rubber growing countries.
Accurate identification of pathogen is important for this
reason. A Phomopsis sp. was isolated as an endophyte from
Hevea brasiliensis in Brazil but the species was not
determined (Rocha et al. 2011).
References: Holliday 1980; Zhuang 2001
Phomopsis javanica Uecker & D.A. Johnson, Mycologia
83(2): 194 (1991)
Disease and host: Shoot blight of Asparagus officinalis
Distribution: Indonesia (Java), Taiwan
Notes: This pathogen is known to be more severe than
Phomopsis asparagi from asparagus and differs from P.
asparagi by producing paraphyses among the conidiophores
and conidiogenous cells. It was, therefore, recognized as a
distinct taxon (Uecker and Johnson 1991).
Reference: Uecker and Johnson 1991
Phomopsis juniperivora G. Hahn [as ‘juniperovora’],
Phytopathology 10: 249 (1920)
Disease and host: Twig blight disease of blight of cedars/
juniper and blight/tip blight of junipers (Juniperus virginiana)
from a nursery grown stock, Juniperus chinesis, J. communis, J. exelsa, J. horizontalis, J. pachyphloea, J. procera, J.
sabina and J. scopulorum
Distribution: UK (Scotland), USA (Kansas, Illinois,
Minnesota, Iowa, Ohio, New York, Pennsylvania)
Notes: Phomopsis thujae Died from Thuja occidentalis
has been compared with P. juniperivora. Several species of
Phomopsis have been recorded from Juniperus. Phomopsis inconstans (Sacc.) Died has been recorded from twigs
of J. communis in Germany and Italy. Phomopsis occulta
Sacc. has been recorded from Juniperus chinensis, J.
excelsa, J. sabina and J. virginiana (Anonymous 1960).
Several undetermined species of Phomopsis have also
been recorded from J. chinensis in California, USA and
Juniperus sp. in British Columbia, Canada (French 1989;
Hilton 2000).
213
Despite the importance of this significant pathogen on
temperate ornamental conifers Phomopsis juniperivora has
not been epitypified. Eight species have been differentiated
from conifers: Phomopsis occulta Trav., Diaporthe conorum
(Desm.) Niessl, P. juniperovora Hahn, P. conorum (Sacc.)
Died., P. montanensis Hahn., P. strobi Syd., P. pseudotsugae
Wilson, P. abietina (Hart.) Wilson & Hahn and P. boycei
Hahn (Hahn 1930). Reassessment of Phomopsis from
conifers awaits investigation and clarification.
References: Hahn 1940, 1943; Wheeler et al. 1975
Phomopsis lantanae (M.E.A. Costa & Sousa da
Câmara) B. Sutton, Coelomycetes: 571 (1980)
Disease and host: Associated with diseases of leaves and
stems of Lantana camera
Distribution: South eastern Brazil, India, Portugal,
Singapore and Zambia
Notes: Lantana camera (Verbanacae) is a well known
invasive species in both tropical and subtropical regions.
Microbiota associated with Lantana camera in eastern
Brazil has been surveyed in order to identify potential
biocontrol agents for this plant. Fifteen fungal species
causing various diseases were associated with Lantana
camera including two Phomopsis species, one of which is
an undescribed species (Pereira and Barreto 2001).
Both alpha and beta conidia were described for Phomopsis lantanae. Phomopsis lantanae-glutinosae Pereira
and Barreto has only alpha conidia (Pereira and Barreto
2001). The occurrence of several different species names
related to one host on the basis of minimal morphological
delineation suggests a need for further clarification by fresh
collection and molecular data.
References: Barreto et al. 1995; Pereira and Barreto
2001
Phomopsis leptostromiformis var. leptostromiformis (J.
G. Kühn) Bubák, in Lind, Danish Fungi: 422 (1913)
Teleomorph : Diaporthe toxica P.M. Will., Highet, W. Gams
& Sivasith., in Williamson, Highet, Gams, Sivasithamparam
& Cowling, Mycol. Res. 98: 1367 (1994)
Phomopsis leptostromiformis var. occidentalis R.G.
Shivas, J.G. Allen & P.M. Will. Mycol. Res. 95: 322 (1991)
Teleomorph: Diaporthe woodii Punith., Mycol. Pap. 136:
51 (1974) (Williamson et al. 1994)
Disease and host: Stem rot, stem cankers, leaf
infections and seed decay of Lupinus angustifolius and
L. cosenfinii and pod blight and seed discoloration of L.
angustifolius, Lupinus albus, L. angustifolius, L. cosentinii, L. pilosus, L. luteus and Trifolium subterraneum
(subterranean clover)
Distribution: Brazil, South Africa, USA (Florida),
Western Australia
Notes: Phomopsis leptostromiformis comprises two
varieties, var. leptostromiformis and var. occidentalis (Kuhn
1913; Shivas et al. 1991). Only P. leptostromiformis. var.
214
occidentalis produced its teleomorph in vitro and it was
recognized as D. woodii Punith. (Wood & Sivasithamparam
1989; Williamson et al. 1994). Observations of fungal
development on infected lupin stubble in the field resulted
in the discovery of the teleomorph of the Phomopsis state
earlier recognized as var. leptostromiformis. A new species,
Diaporthe toxica Will, Highet, Gams & Sivasith was
described for the teleomorph of the toxicogenic Phomopsis
sp. (var. leptostromiformis) (Williamson et al. 1994).
In South Africa, lupinosis of sheep has been shown to be
due to ingestion of lupin (Lupinus luteus, L. angustifolius or
L. albus) stubble or hay on which P. leptostromiformis grows
as a saprobe (Van Warmelo et al. 1970). Subsequently, the
disorder in Australia has been shown to be caused by intake
of lupins contaminated with P. rossiana Sacc. (Wood et al.
1973), which was later recognized as a synonym of P.
leptostromiformis.
Future work is needed to establish the taxa without
confusion.
References: Ostazeski and Wells 1960; van Warmelo and
Marasas 1972; Gorter 1977; Sampson and Walker 1982;
Cowling et al. 1984; Payne 1983; Wood 1986; Uecker
1988; Shivas et al. 1991; Mendes et al. 1998; Cowley et al.
2008
Phomopsis lokoyae G.G. Hahn, Mycologia 25: 374
(1933)
Teleomorph: Diaporthe lokoyae A. Funk (1968)
Disease and host: Associated with the living and dead
cankered trees of Pseudotsuga taxifolia (Douglas fir) and
also with P. menziesii, Arceuthobium tsugense, Metasequoia
glyptostroboides,
Distribution: Canada, USA (California, Oregon)
Notes: Douglas fir (Pinaceae) is important as a temperate
ornamental conifer which is damaged by P. lokoyae. This
pathogen is considered to be a distinct species among the
Phomopsis records from conifers (Hahn 1930) and the
original description confirmed its morphological distinctiveness from P. occulta and P. juniperovora, which also occur on
conifers.
References: Bega 1978; Ginns 1986
Phomopsis longicolla Hobbs, in Hobbs, Schmitthenner
& Kuter, Mycologia 77: 542 (1985)
Disease and host: Associated with soybean seed decay
and isolated from seed, pod and stems of soybean (Glycine
max) (Fabaceae), Abutilon theophrasti (Malvaceae),
Arachis hypogaea (Fabaceae), Chamaesyce nutans
(Euphorbiaceae), Ipomoea lacunosa (Convolvulaceae) and
Xanthium strumarium (Asteraceae)
Distribution: Australia, Croatia, Greece, New Mexico,
USA (Arkansas, Iowa, Illinois, Missouri, Mississippi,
Nebraska, Ohio)
Notes: Phomopsis longicolla was originally described
from soybean, and is morphologically distinct from other
Fungal Diversity (2011) 50:189–225
species recorded from soybean in Ohio and Indiana (USA)
(Hobbs et al. 1985). P. longicolla isolates from different
hosts and different geographical locations, including the
type isolate, were tested on soybean and aggressiveness
was measured as the severity of lesions pod and seed decay
(Li et al. 2010a, b).
Several different species of Phomopsis have been recorded
from soybean and recognized morphologically and by ITS
sequence data. In describing P. longicolla, the authors stated that
P. sojae Lehmann. (Sacc) was the most common species on
soybean. Phomopsis sojae is redescribed and the type materials
of P. glycines Petr. and P. phaseoli Petch were compared (Hobbs
1985). Alpha-conidium length and width measurements for P.
longicolla and P. sojae overlapped, but the mean length-towidth ratios were distinct. The morphological distinct mean
length-to-width ratio was applied as the criterion of species
identification. In conclusion of this work Phomopsis glycines
was regarded as a synonym of P. sojae and P. phaseoli is
considered a nomen dubium, due to lack of informative
structural features from type material (Hobbs et al. 1985).
The validity of these conclusions has been challenged in
several other investigations (Kulik 1984; Kulik and Sinclair
1999; Morgan-Jones 1989) (see the entry under Diaporthe
phaseolarum). The ITS sequence similarity of seven geographically diverse P. longicolla isolates confirmed that they
have a similar evolutionary lineage, with less affiliations to
some D. phaseolorum var. sojae isolates (Zhang et al. 1998)
and can be regarded as a distinct species by molecular data.
References: Vrandecic et al. 2004, 2007; Mengistu et al.
2007; Sanogo and Etarock 2009; Farr and Rossman 2011
Phomopsis longiparaphysata Uecker & K.C. Kuo,
Mycotaxon 44: 426 (1992)
Disease and host: Associated with disease on fruits of
grapevines (Vitis cv. Black Queen)
Distribution: Taiwan.
Notes: This fungus is distinctive for its long, narrow
branched paraphyses and is the second species of Phomopsis
described with paraphyses (Uecker and Kuo 1992). Fresh
collections are needed as this is taxonomically significant
due to its extraordinary morphological feature which would
be a recognizable as any congruent feature with molecular
data with the other taxa recorded with similar features.
Reference: Uecker and Kuo 1992.
Phomopsis oblonga (Desm.) Traverso, Fl. ital. crypt.,
Pars 1: Fungi. Pyrenomycetae. Xylariaceae, Valsaceae,
Ceratostomataceae: 248 (1906)
Teleomorph : Diaporthe eres Nitschke, Pyrenomycetes
Germanici 2: 245 (1870)
Disease and host: Associated with multiple plant hosts
causing cankers, fruit rots and leaf spot diseases. Over 300
plant species, including several economically important
host genera, have been recorded as hosts for D. eres (Farr
and Rossman 2011). P. oblonga is known as an associated
Fungal Diversity (2011) 50:189–225
species with elm trees in the presence of Dutch elm disease
with other possible causative agents.
Distribution: Eastern United States, Europe and other
different geographical locations of the world
Notes: Several secondary metabolites as possible
boring/feeding deterrents for elm bark beetles were
isolated and characterized from P. oblonga from elm
(Claydon et al. 1985).
Wehmeyer (1933) listed a number of synonyms for D.
eres including Phoma, Phomopsis, Sphaeria and Valsa sp.
Some authors have considered this as a species complex
(Farr and Rossman 2011). The complex has to be resolved
by the recollection and identifying the genetically distinct
taxonomic entities.
References: Claydon et al. 1985; Dvořák et al. 2006;
Farr and Rossman 2011
Phomopsis mangiferae S. Ahmad, Sydowia 8: 183
(1954)
Disease and host: Associated with Mangifera indica,
postharvest decay of M. indica, Psidium guajava
Distribution: Africa (Mauritius, Senegal, Seychelles,
Zambia), Asia (Bhutan, Brunei, China, India, Malaysia,
Nepal, Pakistan, Sri Lanka), Australasia and Oceania,
Central America, West Indies (Cuba, Dominica, Trinidad
& Tobago)
Notes: Phomopsis mangiferae is a significantly important post harvest pathogen on fruit especially in tropics.
References: Punithalingam 1993; Chi et al. 2007
Phomopsis mangrovei K.D. Hyde, Mycol. Res. 95: 1149
(1991)
Disease and host: Die back of intertidal prop roots of
Rhizopora apiculata
Distribution: Thailand
Notes: The taxon has not been recorded after the first
record and reassessment is recommended as this is a
pathogen of the mangrove ecosystem.
Reference: Hyde 1991
Phomopsis obscurans (Ellis & Everh.) B. Sutton, Trans.
Br. mycol. Soc. 48: 615 (1965)
Disease and host: Leaf blight of strawberry and on
Photinia serrulata
Distribution: China and other different geographical
locations of the world.
Notes: Reassessment of this species is needed with fresh
collections considering the wide geographical distribution
and importance as a pathogen on this important fruit crop.
References: Shaw 1973; Alfieri et al. 1984; Mendes et
al. 1998; Crous et al. 2000; Cunnington 2003; Chi et al.
2007; Thaung 2008; Bobev 2009
Phomopsis oryzae-sativae Punith., in Punithalingam &
Sharma, Nova Hedwigia 31: 882 (1980) [1979]
Disease and host: Collar rot disease of Oryza sativa (rice)
Distribution: Thailand
215
Notes: Another taxon, recorded from rice grains
in Papua New Guinea was named P. oryzae Punith
(Punithalingam 1975).
Reference: Ou 1985
Phomopsis sclerotioides Kesteren, Neth. Jl Pl. Path. 73:
115 (1966)
Disease and host: Black root rot of Cucurmis sativus,
Citrullus lanatus, Cucurmis ficifolia, C. maxima and C.
moschata from various geographical locations of the
world.
Notes: Only pseudo microsclerotia and pseudo stromata
are found on the plant according to original description.
Phomopsis cucurbitae McKeen has been also recorded
from cucurbits in Canada and was reported to cause fruit
and stem rots. The original material was compared with P.
sclerotioides and shown to be different, P. cucurbitae
having both alpha and beta conidia and no sclerotia
whereas P. sclerotioides has only alpha conidia with
sclerotia (Kesteren 1967).
References: Van Kesteren 1967; Williams and Liu 1976;
Ginns 1986; Pennycook 1989; Hilton 2000; Cappeli et al.
2004; Santos et al. 2010
Phomopsis stipata (Lib.) B. Sutton, Trans. Br. mycol.
Soc. 50: 356 (1967)
Teleomorph: Apiognomonia erythrostoma (Pers.) Höhn.
Disease and host: Leaf spot diseases of Prunus padus
and P. cerasus (Rosaceae), Laurocerasus officinalis var.
caucasica Padus avium, Pistacia vera
Distribution: Austria, France, Russia, Siberia, Ukraine,
USA (California)
Notes: Reassessment is needed to confirm the teleomorph and anamorph connections at the molecular level.
References: Sutton 1980; Melnik and Pystina 1995a, b;
Chen et al. 2002a, b; Dudka et al. 2004
Phomopsis tersa (Sacc.) B. Sutton, Coelomycetes: 573
(1980)
Disease and host: Associated with leaves, stems and fruit
causing postharvest stem end rot of Passiflora edulis and
Passiflora sp.
Distribution: China, Fiji, Malta, Mauritius, Portugal,
Sri Lanka
References: Sutton 1980; Lutchmeah 1992; Chi et al.
2007
Phomopsis theae Petch, Ann. R. bot. Gdns Peradeniya
9: 324 (1925)
Disease and host: Associated with collar and branch
cankers of tea (Camelia sinensis), Camellia sp. and
Diospyros kaki var. domestica
Distribution: Japan, Kenya, Korea Malawi, Papua New
Guinea, Sri Lanka, Tanzania, Uganda, UK
Notes: This pathogen has been reported as a facultative
parasite on 2–8 years-old tea plants in high elevation and
observed in different surveys in Sri Lanka (Holliday 1980).
216
References: Ebbels and Allen 1979; Holliday 1980;
Shaw 1984; Cho and Shin 2004; Jones and Baker 2007;
Kobayashi 2007
Phomopsis theicola Curzi, Atti Ist. bot. R. Univ. Pavia, 3
Sér. 3: 65 (1927)
Teleomorph: Diaporthe neotheicola A.J.L. Phillips & J.
M. Santos, Fungal Diversity 34: 120 (2009)
Disease and host: Associated with Acer negundo, Aspalathus linearis (Rooibos), Camellia sinensis, Euphorbia
pulcherrima, Foeniculum vulgare, Hydrangea macrophylla,
Protea, Prunus, Pyrus, Vitis vinifera,
Distribution: Portugal, South Africa
Notes: Diaporthe theicola Curzi was once thought to be
the teleomorph of P. theicola (Santos and Phillips 2009).
References: Uecker 1988; Mostert et al. 2001a; Van
Rensburg et al. 2006; Santos and Phillips 2009; Santos et
al. 2010
Phomopsis vaccinii Shear, N.E. Stevens & H.F. Bain,
United States Department of Agriculture Technical Bulletin
258: 7–8 (1931)
Teleomorph: Diaporthe vaccinii Shear
Disease and host: Fruit rot and twig blight of Vaccinium sp.
(blueberries), leaf spots of Vaccinium ashei, V. corymbosum,
V. macrocarpon, V. oxycoccos
Distribution: USA (temperate states including Massachusetts,
New Jersey, Oregon, Washington, Wisconsin)
References: Alfieri et al. 1984; Farr et al. 2002a, b; Farr
and Rossman 2011
Phomopsis vexans (Sacc. & P. Syd.) Harter, J. Agric.
Res., Washington 2(5): 338 (1914)
Teleomorph: Diaporthe vexans (Sacc. & P. Syd.) Gratz,
Phytopathology 32: 542 (1942)
Disease and host: Fruit rot, leaf spot, stem blight and tip
over disease of eggplants (Solanum melongena) and other
solanaceous species, Acacia sp. (Fabaceae), Prunus sp.
(Rosaceae), and Sorghum bicolor (Poaceae), Capsicum
annuum and Lycopersicon esculentum
Distribution: The distribution is cosmopolitan.
Notes: Diaporthe vexans, thought to be the teleomorph of
P. vexans, was invalidly published (Art. 59, ICBN) (Rehner
and Uecker. 1994). The teleomorph of the fungus has not yet
been encountered in nature but Gratz (1942) observed
perithecia on 2% potato dextrose agar in culture, and
assigned the name Diaporthe vexans. D. vexans is positioned
as synonymous to P. vexans in Species Fungorum. Another
related name, Phoma solani Halst., may be a nomen nudum
and thus invalid (Farr and Rossman).
References: Tai 1979; Sawada 1959; Farr and Rossman 2011
Phomopsis viticola var. viticola (Sacc.) Sacc., Annls
mycol. 13: 118 (1915).
Disease and host: Phomopsis cane and leaf spot and
infections of pruning wounds of Vitis sp., Ampelopsidis sp.
(Vitaceae). The distribution is cosmopolitan.
Fungal Diversity (2011) 50:189–225
Notes: There was considerable confusion in the
taxonomy of Phomopsis from grapevine (Melanson et
al. 2002; Merrin et al. 1995a, b; Mostert et al. 2001a;
Phillips 1999; Scheper et al. 2000) as several species of
Phomopsis can infect the host and cause variable symptoms in different parts of the grapevines (canes, leaves,
and fruits).
Merrin et al. (1995a, b) studied the variation of
Phomopsis in Australia using morphology, host response
and pectic zymogram analysis and identified two taxa
(Phomopsis taxon 1 and taxon 2), which cause cane and
leaf blight of Vitis sp. Although they considered that
taxon 1 fitted the descriptions of P. viticola, the alpha
conidia are smaller than the range of sizes given (Phillips
1999), therefore taxon 2 was identified as showing more
resemblance to P. viticola in the same study.
Mostert et al. (2000) studied the endophytic fungi
associated with shoots and leaves of Vitis vinifera, with
specific reference to the Phomopsis viticola complex.
The Phomopsis viticola complex had a relative importance of 9% and accounted for 3% of the isolations. P.
viticola was mainly isolated from the nodes and internodes, the plant parts in which P. viticola usually causes
disease symptoms.
To clarify the existing taxonomic confusion within the
P. viticola complex Mostert et al. (2001a) studied the
species occurring on grapevines in South Africa using
morphological, cultural, molecular and pathological characterization. Phomopsis viticola (Phomopsis taxon 2 from
Australia) was found to be the cause of Phomopsis cane
and leaf spot disease, and was neotypified. Three
additional species, Diaporthe perjuncta, P. amygdali and
Phomopsis sp. 1 were also found to be present in South
Africa. Furthermore, the Australian taxon 2 isolate
clustered with P. viticola isolates originating from other
regions of the world (Mostert et al. 2001a). This study
once again reiterates the importance of integrating molecular and morphological techniques in the identification of
species of Phomopsis on grapevines.
Rawnsley et al. (2004) studied pathogenicity of D.
perjuncta and P. viticola in Australia and recognized that
only P. viticola caused brown-black, longitudinal, necrotic
lesions on stem tissue and leaf spots characteristic of the
disease, whereas both D. perjuncta and P. viticola induced
bleaching of dormant canes.
References: Farr and Rossman 2011; Rawnsley 2002
Phomopsis vitimegaspora K.C. Kuo & L.S. Leu,
Mycotaxon 66: 498 (1998)
Teleomorph: Diaporthe kyushuensis Kajitani & Kanem.,
Mycoscience 41: 112 (2000)
Disease and host: Shoot blight, dead arm disease and
swelling arm disease of Vitis vinifera
Distribution: Japan, Taiwan
Fungal Diversity (2011) 50:189–225
Notes: An epitype culture of P. vitmegaspora has been
used in the reassessment of Phomopsis of grapes (van
Niekerk 2005) and was confirmed as distinct from the other
species of Phomopsis recorded on grape from South Africa.
References: Kuo and Leu 1998; Kajitani and Kanematsu
2000
Diaporthe australafricana Crous and van Niekerk
(2005)
Disease and host: Associated with diseases of grapevines
Distribution: Australia, South Africa
Notes: This distinct species has been described in the
latest reassessment of species of Phomopsis of grapevines
for Australian and south African isolates as more or less
resembling D. viticola (van Niekerk et al. 2005). Therefore
the name D. australafricana is proposed for the Australian
isolates formally treated as D. perjuncta or D. viticola.
References: Farr and Rossman 2011
Diaporthe perjuncta Niessl, Hedwigia 15: 153 (1876)
Disease and host: Associated with fallen branches of
Ulmus campestris and U. glabra (Ulmaceae), Vitis vinifera
(Vitaceae)
Distribution: Austria, Australia, Germany, Portugal,
South Africa
Notes: One objective of the reassessment of species of
Phomopsis from grapevines was to clarify the concept of D.
perjuncta (van Niekerk et al. 2005). D. perjuncta is
distinguished from D. viticola and D. australafricana based
on morphology and sequence data. Pathogenicity studies
and endophytic isolation of Diaporthe from grapevine in
Australia (Rawnsley et al. 2004) which has been applied the
name D. perjuncta would be replaced by the name D.
austrlafricana.
References: Phillips 1999; Mostert et al. 2001a
Diaporthe phaseolorum (Cooke & Ellis) Sacc., Syll.
fung. 1: 692 (1882)
Disease and host: Associated with pod and stem blight
of soybean attributed to Diaporthe phaseolorum (Cooke &
Bills) Sacc. var. sojae (Lehman) Wehm., and stem canker
caused by D. phaseolorum var. caulivora Athow &
Caldwell. The taxon also has been recorded from Aeschynomene histrix, Calopogonium mucunoides, Centrosema
acutifolium, C. macrocarpum, C. pubescens, Clitoria
ternatea, Desmodium sp., Glycine ussuriensis, Lablab
purpureus, Macroptilium atropurpureum M. lathyroides,
Macrotyloma axillare, M. uniflorum, and Vigna sp., Aspalathus linearis, Aster sp., Capsicum annuum, Capsicum
frutescens, Cyphomandra betacea, Helianthus annuus as
endophytically in Kandelia candel
Distribution: China, Greece, South Africa, Eastern,
western and southern United States
Notes: The increase in soybean consumption and
cultivation all over the world has been accompanied by an
increase in records of pathogens, among them species
217
belonging to the Diaporthe/Phomopsis complex reviewed
by Morgan-Jones (1989).
The validity of the names P. batatae, P. phaseoli and P.
sojae was discussed by Kulik (1984) who concluded that
they should be one taxon, i.e. Phomopsis phaseoli (Desm.)
Sacc. For similar reasons he considered the teleomorphs
Diaporthe phaseolarum var. batatis, var. sojae and var.
phaseolarum to be synonymous with D. phaseolarum
(Cooke & Ellis) Sacc. However, Hobbs et al. 1985 used
the name Phomopsis sojae for his isolates from Ohio and
stated that only P. phaseoli remained a doubtful name (see
entry under Phomopsis longicolla). Zhang et al. (1997,
1998, 1999) examined isolates of Phomopsis from soybean
for molecular phylogenetic identification and recognized
that morphological characteristics of the isolates, along
with the ITS sequences, suggest that P. longicolla is a
distinct species, whereas D. phaseolorum var. caulivora
and D. phaseolorum var. meridionalis are varieties of D.
phaseolorum, and D. phaseolorum var. sojae are either
several varieties of D. phaseolorum or possibly several
distinct species. Most investigators preferred to conserve
the name Diaporthe phaseolorum and its varieties differentiated on morphological plasticity and molecular variability (Nevena et al. 1997; Kulik 1984; Zhang et al. 1997,
1998).
However, epitypification of either Phomopsis phaseoli
(Desm.) Sacc. (1915) or Phomopsis phaseoli Petch (1922)
is required in order to prevent confusion.
References: Simmonds 1966; French 1989; Pennycook
1989; Lenne 1990; Crous et al. 2000; Mengistu et al. 2007
Diaporthe viticola Nitschke, Pyrenomycetes Germanici
2: 264 (1870)
Disease and host: Cane spot diseases of grapevines in
Europe (Portugal, Germany) and on Hydragea macrophylla.
Distribution: Europe (Portugal, Italy, Germany)
Notes: A phylogenetic analysis of ITS data generated in the
reassessment of grape diseases caused by species of
Phomopsis distinguished three clades containing isolates
previously identified as D. perjuncta. Based on type studies
it was concluded that the name D. viticola can be applied to
collections from Portugal and Germany. The fungus that
Merrin et al. (1995a, b), referred to as Phomopsis taxon 1 on
grapevines was argued to be the same as D. perjuncta by
Phillips (1999). Later, Scheper et al. (2000) again referred to
it as D. viticola. In a subsequent study, Mostert et al. (2001a)
chose to follow Phillips (1999) and used the name D.
perjuncta for taxon 1, however, also noted that minor
morphological differences existed in perithecia and
ascospores between the Portuguese, South African and
Australian material, which confirmed the designation of a
novel taxon, D. australafricana for isolates from Australia
and South Africa.
References: Mostert et al. 2001a, b
218
Concluding remarks
Species concepts within Phomopsis have evolved from
morphological species to phylogenetic and biological
species incorporating molecular data. The rapid advancement of understanding of molecular phylogenies in the
resolution of species for anamorphic fungi has been
utilized to resolve confusion in the taxonomy of Phomopsis and its sexual state. An overview of the current
knowledge of species of Phomopsis provides a foundation
for future taxonomic and phylogenetic studies. The best
practices for the resolution of taxonomy in the genus are
epitypification of existing names and linking the species to
reliable sequence data, which could be achieved by a
collaborative effort among interested groups. Fresh collections
are needed for most of the significant pathogens. Information
on common phytopathogens are important for taxonomists
wanting to identify taxa and are useful for plant pathologists,
plant breeders and quarantine officials in their endeavours in
phytosanitation, plant disease diagnosis, plant breeding and
quarantine measures. With a well resolved phylogeny and
accurately identified species in the genus, scientists will also
be able to extend studies on evolutionary adaptation, coevolution, endophytism, metabolites and the cellular and
molecular scenarios related to pathogenicity.
Acknowledgements This project is supported by the Global
Research Network for Fungal Biology, King Saud University and
State Key Laboratory of Mycology, Institute of Microbiology, the
latter by grant NSFC 30625001. Dhanushka Udayanga thanks the
State Key Laboratory of Mycology, Institute of Microbiology,
Chinese Academy of Sciences, Beijing and the Mushroom
Research Foundation, Chiang Mai, Thailand for a postgraduate
scholarship. Cai Lei (CAS, Beijing) is thanked for the suggestions
to improve the manuscript. Pedro W. Crous (CBS Netherland), HongBing Ma (Shandong Agricultural University, China), and Roger Shivas
(Queensland plant pathology herbarium, Australia) are thanked for
unpublished sequence information and type cultures. Belinda Rawnsley
(South Australian Research and Development Institute: SARDI, Australia), Sam Markell (North Dakota State University, USA) and Thomas
Chase (South Dakota University, USA) are thanked for allowing us to use
the pictures provided.
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