True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. ...Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
Strawberry is a small fruit crop with high economic value. Anthracnose caused by Colletotrichum spp. poses a serious threat to strawberry production, particularly in warm and humid climates, but ...knowledge of pathogen populations in tropical and subtropical regions is limited. To investigate the diversity of infectious agents causing strawberry anthracnose in Taiwan, a disease survey was conducted from 2010 to 2018, and Colletotrichum spp. were identified through morphological characterization and multilocus phylogenetic analysis with internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, chitin synthase, actin, beta-tubulin, calmodulin, and the intergenic region between Apn2 and MAT1-2-1 (ApMAT). Among 52 isolates collected from 24 farms/nurseries in Taiwan, a new species, Colletotrichum miaoliense sp. nov. (6% of all isolates), a species not previously known to be associated with strawberry, Colletotrichum karstii (6%), and three known species, Colletotrichum siamense (75%), Colletotrichum fructicola (11%), and Colletotrichum boninense (2%), were identified. The predominant species C. siamense and C. fructicola exhibited higher mycelial growth rates on potato dextrose agar and caused larger lesions on wounded and non-wounded detached strawberry leaves. Colletotrichum boninense, C. karstii, and C. miaoliense only caused lesions on wounded leaves. Understanding the composition and biology of the pathogen population will help in disease management and resistance breeding.
Brown blight, a destructive foliar disease of tea, has become a highly limiting factor for tea cultivation in Taiwan. To understand the population composition of the causal agents (
spp.), the fungal ...diversity in the main tea-growing regions all over Taiwan was surveyed from 2017 to 2019. A collection of 139
isolates was obtained from 14 tea cultivars in 86 tea plantations. Phylogenic analysis using the ribosomal internal transcribed spacer, glutamine synthetase gene, Apn2-Mat1-2 intergenic spacer, β-tubulin, actin, calmodulin, and glyceraldehyde-3-phosphate dehydrogenase genes together with morphological characterization revealed three species associated with brown blight of tea; namely,
(95.6% of all isolates),
(3.7%), and
(0.7%). This is the first report of
in Taiwan. The optimal growth temperatures were 25°C for
and 25 and 30°C for
and
. Although
and
were more adapted to high temperature,
was the most pathogenic across different temperatures. Regardless of whether spore suspensions or mycelial discs were used, significantly larger lesions and higher disease incidences were observed for wounded than for nonwounded inoculation and for the third and fourth leaves than for the fifth leaves. Wounded inoculation of detached third and fourth tea leaves with mycelial discs was found to be a reliable and efficient method for assessing the pathogenicity of
spp. within 4 days. Preventive application of fungicides or biocontrol agents immediately after tea pruning and at a young leaf stage would help control the disease.
Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated ...extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus
Phyllosticta
(Dothideomycetes, Botryosphaeriales). Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.
Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (
L.) is one of the key and oldest ...vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving
and
taxa. In addition, genera such as
and
were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.
Pleosporales species are important plant pathogens, saprobes, and endophytes on a wide range of economically important plant hosts. The classification of Pleosporales has undergone various ...modifications in recent years due to the addition of many families described from multiple habitats with a high level of morphological deviation. Numerous asexual genera have been described in Pleosporales that can be either hyphomyceteous or coelomycetous. Phoma- or coniothyrium-like species are common and have been revealed as polyphyletic in the order Pleosporales and linked with several sexual genera. A total of 31 pleosporalean strains were isolated in different regions of Taiwan between 2017 and 2018 from the leaves of Camellia sinensis plants with symptoms of leaf spot disease. These strains were evaluated morphologically and genotypically using multi-locus sequence analyses of the ITS, LSU, SSU, rpb2, tef1 and tub2 genes. The results demonstrated the affiliation of these strains with the various families in Pleosporales and revealed the presence of one new genus (Neoshiraia) and eight new species (Alloconiothyrium camelliae, Amorocoelophoma camelliae, Leucaenicola camelliae, L. taiwanensis, Neoshiraia camelliae, N. taiwanensis, Paraconiothyrium camelliae and Paraphaeosphaeria camelliae). Furthermore, to the best of our understanding, Didymella segeticola, Ectophoma pomi and Roussoella mexican were reported for the first time from C. sinensis in Taiwan.
The genera Lophiostoma, Misturatosphaeria and several other allied taxa in Lophiostomataceae are revisited. Accounts of these taxa, including their history, morphology, and family placement, based on ...molecular phylogeny, are provided. Type or representative specimens of Lophiostoma and Misturatosphaeria were examined and fresh specimens were obtained from Germany, Italy, Japan and Thailand. A multi-gene phylogenetic analysis of the lophiostomataceous genera Floricola, Lophiostoma, Misturatosphaeria and related taxa is provided. Sixteen genera including Lophiostoma, Lophiohelichrysum, Dimorphiopsis, Platystomum and Vaginatispora, plus eleven newly introduced genera Biappendiculispora, Alpestrisphaeria, Capulatispora, Coelodictyosporium, Guttulispora, Lophiopoacea, Neotrematosphaeria, Paucispora, Pseudolophiostoma, Pseudoplatystomum and Sigarispora are accepted in Lophiostomataceae based on morphology and phylogeny. Lophiostoma caulium, Lophiostoma arundinis and Lophiostoma caudatum are accommodated in Sigarispora. Lophiostoma winteri and Lophiostoma fuckelii are placed in the genera Lophiopoacea and Vaginatispora respectively. Three Curreya species and Misturatosphaeria claviformis are transferred to a new genus, Neocurreya. All other Misturatosphaeria species except Misturatosphaeria aurantiinotata and M. uniseptata are separated in the new genera Asymmetrispora, Aurantiascoma, Magnibotryascoma, Pseudoaurantiascoma and Pseudomisturatosphaeria based on their morphological and phylogenetic affinities. Another new genus, Ramusculicola is introduced for a new collection from Thailand. These seven new genera are accommodated in a new family Floricolaceae, together with Floricola and Misturatosphaeria. Several massarina-like species clustered as a sister clade to Amorosia littoralis and are accommodated in a new genus Angustimassarina. A new family Amorosiaceae is proposed to accommodate the genera Amorosia and Angustimassarina. The putatively named species Decaisnella formosa and Thyridaria macrostomoides form a separate clade together with a new genus Lignosphaeria which is placed in Dothideomycetes, genera incertae sedis.
The family
Pleosporaceae
includes numerous saprobic, opportunistic human, and plant pathogenic taxa. The classification of genera and species
Pleosporaceae
has been a major challenge due to the lack ...of a clear understanding of the importance of the morphological characters used to distinguish taxa as well as the lack of reference strains. Recent treatments concluded that
Pleospora
and some other genera in
Pleosporaceae
are likely polyphyletic. In order to establish the evolutionary relationships and to resolve the polyphyletic nature of
Pleospora
and allied genera, we sequenced the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions of
Pleosporaceae
species and phylogenetically analysed this data. Multigene phylogenies strongly support the monophyletic nature of
Pleosporaceae
among the other families in
Pleosporale
s, and the acceptance of the genera
Alternaria, Bipolaris, Clathrospora, Comoclathris, Curvularia, Dactuliophora, Decorospora, Diademosa, Exserohilum, Extrawettsteinina, Gibbago, Neocamarosporium, Paradendryphiella, Platysporoides, Pleospora, Porocercospora, Pseudoyuconia
and
Pyrenophora. Austropleospora
,
Dendryphion
,
Edenia
and
Macrospora
are excluded from the family based on morphology coupled with molecular data. Two novel species,
Alternaria murispora
in this paper and
Comoclathris sedi
are introduced. The sexual morph of
Alternaria alternata
is re-described and illustrated using modern concepts from fresh collections. The paraphyletic nature of
Pleospora
is resolved based on the available morpho-molecular data, but further sampling with fresh collections, reference or ex-type strains and molecular data are needed to obtain a natural classification of genera and the family.
The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal ...groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.
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