The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like taxa, which is ...between 2.6 and 4.5% of the estimated species. Several forums such as Botanica Marina series, Fungal Diversity notes, Fungal Biodiversity Profiles, Fungal Systematics and Evolution—New and Interesting Fungi, Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade. The need to define a fungal species more accurately has been recognized, but there is much research needed before this can be better clarified. We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding. Some genera are barely known, whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing. In this paper, we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus. The genera are the ascomycetes
Colletotrichum
and
Pestalotiopsis
(with many species or complexes),
Atrocalyx
,
Dothiora, Lignosphaeria
,
Okeanomyces, Rhamphoriopsis
,
Thozetella
,
Thyrostroma
(relatively poorly studied genera) and the basidiomycete genus
Lepiota
. We provide examples where knowledge is incomplete or lacking and suggest areas needing further research. These include (1) the need to establish what is a species, (2) the need to establish how host-specific fungi are, not in highly disturbed urban areas, but in pristine or relatively undisturbed forests, and (3) the need to establish if species in different continents, islands, countries or regions are different, or if the same fungi occur worldwide? Finally, we conclude whether we are anywhere near to flattening the curve in new species description.
Colletotrichum
is one of the most important plant pathogenic genera that is responsible for numerous diseases which can have a profound impact on the agricultural sector. Species delineation is ...difficult due to a lack of distinctive phenotypic variation. Therefore, in this study three different genomic approaches based on phylogenetic, evolutionary and coalescent-based methods are applied to establish robust species boundaries. The reliability of five different DNA barcodes was also assessed to provide further insights into species delineation. The ITS region can resolve the placement of taxa up to the species complex level. The
GAPDH
and
TUB2
markers are determined to be the most informative for most complexes. However, no single marker could discriminate between species in all complexes, therefore different molecular approaches based on multi-locus datasets are recommended. This is the first study to provide an estimated divergence time for all species complexes in
Colletotrichum.
The estimated divergence time for species complexes ranged between 4.8 to 32.2 MYA
.
Based on the high level of congruent results obtained from the different molecular approaches, a new species complex, the
Colletotrichum agaves
complex is introduced. This complex consists of five taxa which are characterised by the presence of straight or slightly curved conidia with obtuse apices. This study shows that coalescent approaches and multi-locus phylogeny are crucial to establish species boundaries in
Colletotrichum
. The taxonomic placement of three singleton taxa
Colletotrichum axonopodi, C. cariniferi
and
C. parallelophorum
is revised. We accept 248 species and provide recommendations regarding species boundaries in the graminicola–caudatum complex.
Bipolaris
species are important plant pathogens with a worldwide distribution in tropical and temperate environments. Species recognition in
Bipolaris
has been problematic due to a lack of molecular ...data from ex-type cultures, the use of few gene regions for species resolution and overlapping morphological characters. In this study, we evaluate the efficiency of different DNA barcodes in species delimitation in
Bipolaris
by phylogenetic analyses, Automatic Barcode Gap Discovery and Objective Clustering. GAPDH is determined to be the best single marker for the genus. These approaches are used to clarify the taxonomic placement of all sequences currently named as
Bipolaris
in GenBank based on ITS and GAPDH gene sequence data. In checking various publications, we found that the majority of new host records of fungal species published in the Plant Disease journal from 2010 to 2019 were based on BLAST searches of the ITS sequences and up to 82% of those records could be erroneous. Therefore, relying on BLAST searches from GenBank to name species is not recommended. Editorial boards of journals and reviewers of new record papers should be aware of this problem. In naming
Bipolaris
species, whether new or known, it is recommended to perform phylogenetic analyses based on GAPDH using the correct taxon sampling for accurate results and the species relationship should have reliable statistical support. At least two new species are represented by molecular data in GenBank and we provide an updated taxonomic revision of
Bipolaris
. We accept 45 species in
Bipolaris
and notes are provided for all the species including hosts and geographic distribution.
Fungi are an essential component of any ecosystem and have diverse ecological roles, ranging from endophytes to epiphytes and pathogens to saprobes. The current estimate of fungal endophytes is ...around 1 million species, however, we estimate that there is likely over 3 million species and only about 150,000 fungal species have been named and classified to date. Endophytes inhabit internal plant tissues without causing apparent harm to the hosts. Endophytes occur in almost every plant from the coldest climates to the tropics. They are thought to provide several benefits to host plants and improve the hosts’ ability to tolerate several abiotic and biotic stresses. Endophytes produce secondary metabolites with biotechnological, industrial and pharmaceutical application. Some endophytes appear to be host-specific, while some are associated with a wide range of hosts. We discuss the importance of endophytes. The ability to switch lifestyles from endophytes to pathogens or saprobes is discussed. Interactions between endophytes and hosts based on fossil data is also highlighted. Factors that influence the specificity in endophytes are discussed. We argue that the endophytic lifestyle is a common strategy in most fungi and that all fungi have endophytic ancestors. We critically evaluate the influence of co-evolution based on fossil data. We hypothesise the influence of specificity on the estimated number of endophytes and overall species numbers, and present examples of metabolites that they produce. We argue that studying endophytes for novel compounds has limitations as the genera recovered are limited. However, if saprobes were chosen instead, this would result in a much higher species diversity and undoubtedly chemical diversity.
The cosmopolitan plant genus
Clematis
contains many climbing species that can be found worldwide. The genus occurs in the wild and is grown commercially for horticulture. Microfungi on
Clematis
were ...collected from Belgium, China, Italy, Thailand and the UK. They are characterized by morphology and analyses of gene sequence data using an integrated species concept to validate identifications. The study revealed two new families, 12 new genera, 50 new species, 26 new host records with one dimorphic character report, and ten species are transferred to other genera. The new families revealed by multigene phylogeny are Longiostiolaceae and Pseudomassarinaceae in Pleosporales (Dothideomycetes). New genera are
Anthodidymella
(Didymellaceae),
Anthosulcatispora
and
Parasulcatispora
(Sulcatisporaceae),
Fusiformispora
(Amniculicolaceae),
Longispora
(Phaeosphaeriaceae),
Neobyssosphaeria
(Melanommataceae),
Neoleptosporella
(
Chaetosphaeriales
, genera
incertae sedis)
,
Neostictis
(Stictidaceae),
Pseudohelminthosporium
(Neomassarinaceae),
Pseudomassarina
(Pseudomassarinaceae),
Sclerenchymomyces
(Leptosphaeriaceae) and
Xenoplectosphaerella
(Plectosphaerellaceae). The newly described species are
Alloleptosphaeria clematidis
,
Anthodidymella ranunculacearum
,
Anthosulcatispora subglobosa
,
Aquadictyospora clematidis
,
Brunneofusispora clematidis
,
Chaetosphaeronema clematidicola
,
C. clematidis
,
Chromolaenicola clematidis
,
Diaporthe clematidina
,
Dictyocheirospora clematidis
,
Distoseptispora clematidis
,
Floricola clematidis
,
Fusiformispora clematidis
,
Hermatomyces clematidis
,
Leptospora clematidis
,
Longispora clematidis
,
Massariosphaeria clematidis
,
Melomastia clematidis
,
M. fulvicomae
,
Neobyssosphaeria clematidis
,
Neoleptosporella clematidis
,
Neoroussoella clematidis
,
N. fulvicomae
,
Neostictis nigricans, Neovaginatispora clematidis
,
Parasulcatispora clematidis
,
Parathyridaria clematidis, P. serratifoliae
,
P. virginianae
,
Periconia verrucose
,
Phomatospora uniseriata
,
Pleopunctum clematidis
,
Pseudocapulatispora clematidis
,
Pseudocoleophoma clematidis
,
Pseudohelminthosporium clematidis
,
Pseudolophiostoma chiangraiense
,
P. clematidis
,
Pseudomassarina clematidis
,
Ramusculicola clematidis
,
Sarocladium clematidis
,
Sclerenchymomyces clematidis
,
Sigarispora clematidicola
,
S. clematidis
,
S. montanae
,
Sordaria clematidis
,
Stemphylium clematidis
,
Wojnowiciella clematidis
,
Xenodidymella clematidis
,
Xenomassariosphaeria clematidis
and
Xenoplectosphaerella clematidis.
The following fungi are recorded on
Clematis
species for the first time:
Angustimassarina rosarum
,
Dendryphion europaeum
,
Dermatiopleospora mariae
,
Diaporthe ravennica
,
D. rudis
,
Dichotomopilus ramosissimum
,
Dictyocheirospora xishuangbannaensis
,
Didymosphaeria rubi
-
ulmifolii
,
Fitzroyomyces cyperacearum
,
Fusarium celtidicola
,
Leptospora thailandica
,
Memnoniella oblongispora
,
Neodidymelliopsis longicolla
,
Neoeutypella baoshanensis
,
Neoroussoella heveae
,
Nigrograna chromolaenae
,
N. obliqua
,
Pestalotiopsis verruculosa
,
Pseudoberkleasmium chiangmaiense
,
Pseudoophiobolus rosae
,
Pseudoroussoella chromolaenae
,
P. elaeicola
,
Ramusculicola thailandica
,
Stemphylium vesicarium
and
Torula chromolaenae
. The new combinations are
Anthodidymella clematidis
(≡
Didymella clematidis
),
A. vitalbina
(≡
Didymella vitalbina
),
Anthosulcatispora brunnea
(≡
Neobambusicola brunnea
),
Fuscohypha kunmingensis
(≡
Plectosphaerella kunmingensis
),
Magnibotryascoma rubriostiolata
(≡
Teichospora rubriostiolata
),
Pararoussoella mangrovei
(≡
Roussoella mangrovei
),
Pseudoneoconiothyrium euonymi
(≡
Roussoella euonymi
),
Sclerenchymomyces jonesii
(≡
Neoleptosphaeria jonesii
),
Stemphylium rosae
(≡
Pleospora rosae)
, and
S. rosae
-
caninae
(≡
Pleospora rosae
-
caninae
). The microfungi on
Clematis
is distributed in several classes of Ascomycota. The analyses are based on morphological examination of specimens, coupled with phylogenetic sequence data. To the best of our knowledge, the consolidated species concept approach is recommended in validating species.
Fungi play vital roles in ecosystems as endophytes, pathogens and saprobes. The current estimate of fungal diversity is highly uncertain, ranging from 1.5 to 12 million, but only around 150,000 ...species have been named and classified to date. Since the introduction of DNA based methods for species identification, the number of newly described taxa has increased from approximately 1000 to around 2000 yearly. This demonstrates the importance of DNA based methods to identify and distinguish species, especially cryptic species. Many novel species from recent studies have been found in historically understudied regions and habitats, but these still represent only a small percentage of the estimated species. In this paper, we examine 16 genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in each genus. The genera treated herein are
Cercospora, Diaporthe, Meliola, Passalora, Phyllachora
,
Phyllosticta, Pseudocercospora, Ramularia
(ascomycetes) and
Cortinarius
,
Entoloma
,
Inocybe
,
Marasmius
,
Psathyrella
,
Puccinia, Russula, Uromyces
(basidiomycetes). We critically evaluate the number of species in these genera and correlate these numbers with the number of entries in GenBank. We introduce 18 new species
Apiospora multiloculata
,
Candolleomyces thailandensis
,
Cortinarius acutoproximus, Cortinarius melleoalbus, Cortinarius pacificus, Cortinarius parvoacetosus, Diaporthe guizhouensis
,
Entoloma pseudosubcorvinum
,
Inocybe meirensongia, Marasmius albulus, Marasmius obscuroaurantiacus, Meliola camporesii
,
Phyllachora siamensis
,
Phyllosticta doitungensis, Picipes yuxiensis
,
Pseudocercospora vignae, Puccinia maureanui
and
Russula inornata
. We also introduce a new record of
Candolleomyces cladii-marisci
and
Inocybe iringolkavensis
. We discuss the genera
Colletotrichum
and
Pleurotus
that are speciose, but do not occur in the top 40. We hypothesize whether there might be more species in these genera and discuss why these genera have some of the largest number of species.
The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around ...150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are
Apiospora
,
Bambusicola
,
Beltrania
,
Capronia
,
Distoseptispora
,
Endocalyx
,
Neocatenulostroma
,
Neodeightonia
,
Paraconiothyrium
,
Peroneutypa
,
Phaeoacremonium
and
Vanakripa
. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
Immotthia
is a poorly known genus, and currently, no DNA sequence data are available to ascertain its proper phylogenetic placement and evolutionary relationships with other bitunicate fungi. To ...date, there are only two species accepted in the genus. During our ongoing research study of bambusicolous fungi in southwest China and Thailand, a fungus associated with stromata of
Hypoxylon
sp. was found on dead bamboo culms in Loei Province, Thailand. Preliminary morphological identification revealed that the fungal collection belongs to
Immotthia
. A novel species,
Immotthia bambusae
, is introduced herein based on a comparison of morphological characteristics with the type specimen of
I. hypoxylon
(≡
Amphisphaeria hypoxylon
Ellis and Everh.), a synonym of
I. atrograna
(Cooke and Ellis) M. E. Barr. Phylogenetic analyses of a concatenated ITS, LSU, SSU, and TEF1-α DNA sequence matrix showed that
Immotthia
belongs to Dictyosporiaceae, Pleosporales. Despite
I. bambusae
strains constituting a supported subclade, they are nested with the genus
Pseudocoleophoma
.
Pseudocoleophoma clematidis
is morphologically different from all other
Pseudocoleophoma
species, while its conidial characteristics are similar to
Cyclothyriella
. Multigene phylogenetic analyses showed that
P. clematidis
formed a clade basal to
Immotthia
, separated from
Pseudocoleophoma
with strong statistical support. Therefore, we introduce a monotypic genus,
Pseudocyclothyriella
Phukhams. and Phookamsak, gen. nov. to accommodate the single species,
Pseudocyclothyriella clematidis
(Phukhams. and K. D. Hyde) Phukhams. and Phookamsak, comb. nov. Detailed descriptions, color micrographs, and phylogenetic trees to show the placement of the new taxa are provided. In addition, an updated taxonomic treatment of the genera
Immotthia
and
Pseudocyclothyriella
is also provided based on the study of the type materials and phylogeny generated from DNA sequence data.
Two novel
species were identified from dicotyledonous plants (
sp. and
) in China. The results were supported by morphological characters and Maximum Likelihood (ML) and Bayesian Inference (BI) ...analyses. Multi-gene phylogenetic analyses of the ITS, LSU, SSU and
2 sequences revealed two new species
and
, which are phylogenetically distinct. The new species are phylogenetically closely related to
However, they are distinguishable from
by having comparatively larger asci and ascospores. This study improves our knowledge of
as no species has been previously described from China. This suggests such taxa may be rare and it is likely that new taxa will be discovered from hosts and environments that have not yet been extensively investigated.
Fungi have evolved diverse strategies to acquire nutrients as endophytes, saprobes, symbionts, or pathogens. Appressoria have been intensively studied due to their importance in attaching and ...breaching the host surface. These specialized infection structures have evolved into various morpho-types: proto-appressoria, hyaline appressoria, melanized (dark) appressoria, and compound appressoria. In this review, we discuss the differences in the formation, differentiation, and function of appressoria among fungi with diverse life strategies. Using DNA sequence information, LSU, 5.8S, SSU and
rpb2
gene fragments, we reconstructed the ancestral states for appressorial types in the main phyla of fungi and fungus-like organisms and found that the hyaline appressoria was the most ancestral form. Our analysis estimated proto-appressoria diversification during the Mesozoic period (92–239 million years ago), however, its origin remains inconclusive. Our data suggest that these hyaline appressoria diversified into melanized or compound appressoria, with evidence of adaptive radiation.
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