Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and ...high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study ...was to resolve the taxonomy and phylogeny of a large collection of Diaporthe
species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation
factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda,
D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii
is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In
contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.
Although Glomerella glycines, Colletotrichum magnum and C. orchidearum are known as causal agents of anthracnose of soybean, Cucurbitaceae and Orchidaceae, respectively, their taxonomy remains ...unresolved. In preliminary analyses based on ITS, strains of these species appear basal in Colletotrichum phylogenies, clustering close to C. cliviae, C. brevisporum and other recently described species from tropical or subtropical regions. Phylogenetic analyses (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 102 strains previously identified as Ga. glycines, C. magnum and C. orchidearum as well as other related strains from different culture collections and studies placed these taxa in three species complexes, and distinguished at least 24 species, including 11 new species. In this study, C. magnum, C. orchidearum and C. piperis were epitypified and their taxonomy resolved, while C. cliviicola was proposed as a new name for C. cliviae. Furthermore, a sexual morph was observed for C. yunnanense, while C. brevisporum, C. cliviicola and C. tropicicola were reported from new hosts or countries. Regarding their conidial morphology, species in the C. dracaenophilum, C. magnum and C. orchidearum species complexes are reminiscent of C. gloeosporioides or C. boninense s. lat., and were likely to be confused with them in the past.
Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and ...non-pathogenic strains. However, in its current concept F. oxysporum is
a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance
and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with
the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.
The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent ...phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae ( Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S . hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.
The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and ...endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.
The genus Cladosporium Bensch, K.; Braun, U.; Groenewald, J.Z. ...
Studies in mycology,
06/2012, Volume:
72, Issue:
1
Journal Article
Peer reviewed
Open access
A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with ...notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.
Taxonomic novelties:Cladosporium allicinum (Fr.: Fr.) Bensch, U. Braun & Crous, comb. nov., C. astroideum var. catalinense U. Braun, var. nov., Fusicladium tectonicola (Yong H. He & Z.Y. Zhang) U. Braun & Bensch, comb. nov., Septoidium uleanum (Henn.) U. Braun, comb. nov., Zasmidium adeniae (Hansf.) U. Braun, comb. nov., Zasmidium dianellae (Sawada & Katsuki) U. Braun, comb. nov., Zasmidium lythri (Westend.) U. Braun & H.D. Shin, comb. nov., Zasmidium wikstroemiae (Petch) U. Braun, comb. nov.
Generic concepts in Nectriaceae Lombard, L.; van der Merwe, N.A.; Groenewald, J.Z. ...
Studies in mycology,
03/2015, Volume:
80, Issue:
1
Journal Article
Peer reviewed
Open access
The ascomycete family Nectriaceae (Hypocreales) includes numerous important plant and human pathogens, as well as several species used extensively in industrial and commercial applications as ...biodegraders and biocontrol agents. Members of the family are unified by phenotypic characters such as uniloculate ascomata that are yellow, orange-red to purple, and with phialidic asexual morphs. The generic concepts in Nectriaceae are poorly defined, since DNA sequence data have not been available for many of these genera. To address this issue we performed a multi-gene phylogenetic analysis using partial sequences for the 28S large subunit (LSU) nrDNA, the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), the large subunit of the ATP citrate lyase (acl1), the RNA polymerase II largest subunit (rpb1), RNA polymerase II second largest subunit (rpb2), α-actin (act), β-tubulin (tub2), calmodulin (cmdA), histone H3 (his3), and translation elongation factor 1-alpha (tef1) gene regions for available type and authentic strains representing known genera in Nectriaceae, including several genera for which no sequence data were previously available. Supported by morphological observations, the data resolved 47 genera in the Nectriaceae. We re-evaluated the status of several genera, which resulted in the introduction of six new genera to accommodate species that were initially classified based solely on morphological characters. Several generic names are proposed for synonymy based on the abolishment of dual nomenclature. Additionally, a new family is introduced for two genera that were previously accommodated in the Nectriaceae.
Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. ...Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum.
Taxonomic novelties:New combinations - Colletotrichum limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. lupini (Bondar) Damm, P.F. Cannon & Crous, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. New species - C. acerbum Damm, P.F. Cannon & Crous, C. australe Damm, P.F. Cannon & Crous, C. brisbanense Damm, P.F. Cannon & Crous, C. cosmi Damm, P.F. Cannon & Crous, C. costaricense Damm, P.F. Cannon & Crous, C. cuscutae Damm, P.F. Cannon & Crous, C. guajavae Damm, P.F. Cannon & Crous, C. indonesiense Damm, P.F. Cannon & Crous, C. johnstonii Damm, P.F. Cannon & Crous, C. kinghornii Damm, P.F. Cannon & Crous, C. laticiphilum Damm, P.F. Cannon & Crous, C. melonis Damm, P.F. Cannon & Crous, C. orchidophilum Damm, P.F. Cannon & Crous, C. paxtonii Damm, P.F. Cannon & Crous, C. pseudoacutatum Damm, P.F. Cannon & Crous C. pyricola Damm, P.F. Cannon & Crous, C. rhombiforme Damm, P.F. Cannon & Crous, C. scovillei Damm, P.F. Cannon & Crous, C. sloanei Damm, P.F. Cannon & Crous, C. tamarilloi Damm, P.F. Cannon & Crous, C. walleri Damm, P.F. Cannon & Crous. Typifications: Epitypifications - C. acutatum J.H. Simmonds, C. limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. nymphaeae (Pass.) Aa, C. phormii (Henn.) D.F. Farr & Rossman, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. Lectotypifications - C. nymphaeae (Pass.) Aa, C. orchidearum Allesch.
The genus Neocosmospora (Fusarium solani species complex) contains saprobes, plant endophytes and pathogens of major economic significance as well as opportunistic animal pathogens. Advances in ...biological and phylogenetic species recognition revealed a rich species diversity
which has largely remained understudied. Most of the currently recognised species lack formal descriptions and Latin names, while the taxonomic utility of old names is hampered by the lack of nomenclatural type specimens. Therefore, to stabilise the taxonomy and nomenclature of these important
taxa, we examined type specimens and representative cultures of several old names by means of morphology and phylogenetic analyses based on rDNA (ITS and LSU), rpb2 and tef1 sequences. Sixty-eight species are accepted in Neocosmospora, 29 of them described herein as new;
while 13 new combinations are made. Eleven additional phylogenetic species are recognized, but remain as yet undescribed. Lectotypes are proposed for eight species, seven species are epitypified and two species are neotypified. Notes on an additional 17 doubtful or excluded taxa are provided.
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