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Tubeufiaceae phylogeny of one of 33 most parsimonious trees generated from a MP analysis of LSU sequence data for 75 taxa showing the phylogenetic placement of six Acanthostigma species within the family (L 5 590.91 steps, CI 5 0.550, RI 5 0.840, RCI 5 0.462). The three newly described species are in boldface. Thickened branches indicate Bayesian posterior probabilities $95%, while numbers above or below branches refer to MP bootstrap values $70%. Two species of Hysteropatella and two species of Botryosphaeria are outgroups.
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Three new bitunicate ascomycetes belonging to the genus Acanthostigma are described from terrestrial decomposing wood collected from Great Smoky Mountains National Park, USA. Phylogenetic analyses of the nuclear ribosomal 28S large subunit and internal transcribed spacer region placed all three species in the Tubeufiaceae and confirmed morphologica...
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... delimited and recoded, resulting in 115 parsimony informative characters. The MP analysis generated 33 most parsimonious trees, which differed only slightly in topology due to equally parsimonious rearrange- ments among taxa with little or no bp differences (e.g. within Tubeufia paludosa clade). (One of these most parsimonious trees is shown in FIG. 24.) The ML analysis generated three most likely trees, which did not differ significantly from one another or from the most parsimonious trees (data not shown). The ITS dataset consisted of 56 taxa and 698 characters of which 582 were excluded. Three of the nine ambiguously aligned regions were recoded, resulting in 87 parsimony ...
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... Notes: In the combined phylogenetic analyses (LSu, ITS, tef 1-α, and rpb2), our isolate clustered with Acanthostigmina multiseptatum (ANM 665) with 91 ML/0.97 PP statistical support. Acanthostigmina multiseptatum was originally introduced as A. multiseptatum based on phylogenetic analyses along with unique morphological features, such as having longer asci and longer ascospores with more septa (Promputtha et al. 2010). Based on morphomolecular studies, Boonmee et al. (2014) transferred this species to Acanthostigmina. ...
... The helicosporous Acanthostigmina multiseptatum was introduced in this study as the asexual morph of A. multiseptatum (Figure 3). Acanthostigmina multiseptatum was introduced from the uSA on wood in mixed coniferousdeciduous forests (Promputtha et al. 2010). The taxon was initially characterized by superficial, scattered or gregarious, globose to subglobose, densely setose, non-collapsing ascomata with 130-380 mm diam, one-celled or septate setae, cylindrical-clavate to clavate asci and fusiform, hyaline ascospores with 14-18-septate (Promputtha et al. 2010). ...
... Acanthostigmina multiseptatum was introduced from the uSA on wood in mixed coniferousdeciduous forests (Promputtha et al. 2010). The taxon was initially characterized by superficial, scattered or gregarious, globose to subglobose, densely setose, non-collapsing ascomata with 130-380 mm diam, one-celled or septate setae, cylindrical-clavate to clavate asci and fusiform, hyaline ascospores with 14-18-septate (Promputtha et al. 2010). Acanthostigmina multiseptatum is differentiated from the extant species of the genus by the large number of septa per ascospores (Promputtha & Miller 2010), and all the taxa in the genus were identified in their sexual state. ...
Tubeufiaceae species have diverse morphologies and habitats and are distributed in both tropical and temperate regions. In the past decade, several new and interesting Tubeufiaceae species were reported from China in aquatic and terrestrial habitats. In this study, we investigated two saprobic species collected on decaying wood in a terrestrial habitat of Xizang Autonomous Region, China. Through phylogenetic analyses of a combined ITS, LSU, tef1-α, and rpb2 dataset coupled with detailed morphological examinations, a novel species within Neomanoharachariella was identified. Phylogenetic analyses revealed that this new species formed a sister clade to Neomanoharachariella aquatica, but can be morphologically distinguished by its pale brown, septate, and flexuous conidiophores, alongside dark brown setae that turn hyaline at the apex and distinct muriform conidia. In addition, this study presents the first asexual and geographical record of Acanthostigmina (A. multiseptatum) from China. Acanthostigmina multiseptatum is characterized by micronematous, hyaline, and septate conidiophores with unique pleurogenous and helicoid conidia.
... This was followed with a final extension step of 72 °C for 7 min and later left at 10 °C as the hold tempt for further used. This procedure was carried out using a modified method of Schoch et al., (2012) [26] and Promputtha and Miller (2010) [22] . The amplicon from the reaction was loaded on 1.5% agarose gel tank (Compact L/XL Biometra by Analytik Jena Company). ...
... This was followed with a final extension step of 72 °C for 7 min and later left at 10 °C as the hold tempt for further used. This procedure was carried out using a modified method of Schoch et al., (2012) [26] and Promputtha and Miller (2010) [22] . The amplicon from the reaction was loaded on 1.5% agarose gel tank (Compact L/XL Biometra by Analytik Jena Company). ...
This study was to carry out the molecular characterization of isolated bacterial from some deteriorated fruits and vegetables. Common bacterial affecting selected fruits and vegetables were isolated. They include: Pseudomonas aeruginosa, Salmonella enterica, Enterococcus faecium and Lactobacillus plantarum. They were molecularly characterized using 16SrDNA sequence analyses. DNA extraction was carried out using Zymo DNA mini kit prep and the primer used were 16SF and 16SR. The 16SrDNA regions of these pathogens were amplified by polymerase chain reaction (PCR) with Gene Amp 9700 thermocycler and then sequenced using Applied Biosystem 3130X gene analyser. Nucleotide sequences were deciphered using nBLAST. Alignment and construction of phylogenetic tree were performed using Neighbour Joining method of MEGA 7 software together with the sequence of related strains which were downloaded from GenBank. The results of the DNA yield and purity were within the range of 23 to 215.2 ng/μl and 1.84 to 1.93. The number of nucleotide for all the organisms isolated varies from 490 to 1563, BLAST searches revealed that the organisms identified were within the range of 93-100% identical. The results demonstrated that good yield and pure DNA extracts were obtained from the selected fruits and vegetables and the primers used are useful for bacterial identification.
... Helicosporous hyphomycetes are the most common asexual morph in the order Tubeufiales, and most of these genera have been shown to be polyphyletic (Tui et al. 2006, Promputtha & Miller 2010, Sánchez et al. 2012. Tubeufia species are widely distributed in freshwater and terrestrial habitats. ...
Diversity of lignicolous freshwater fungi in northwestern Yunnan, China is currently being studied. Four fresh collections of tubeufiaceous taxa were collected and identified. Among of them, Parahelicomyces yunnanensis sp. nov and Tubeufia nigroseptum sp. nov. are introduced as new species based on morphology and molecular phylogenetic analysis of combined ITS, SSU, TEF1-α and RPB2 sequence data. The detailed descriptions and illustrations of the new species are provided, as well as the morphological comparison with similar taxa are discussed. Two strains of Neohelicomyces aquaticus and Tubeufia cylindrothecia are provided.
... Extraction, amplification and sequencing of DNA followed Promputtha and Miller (2010). Briefly, DNA was extracted directly from ~30 ascomata using an E.Z.N.A. ® Microelute Genomic DNA kit (Omega Bio-tek). ...
... Besides the morphological studies, the identity of the novel species was confirmed through phylogenetic studies using DNA extracted directly from the ascomata. Although it is a highly destructive method, it turns out to be the only option when the specimens cannot be cultivated (Jayasiri et al. 2015;Promputtha & Miller 2010;Zeng et al. 2018). Our findings increase the number of Capronia species known in Argentina to eight. ...
Three new species belonging to Capronia are described from plants native to the Andean Patagonian forests, Argentina. The first record of C. chlorospora in South America is also reported. The identity of the three new species is based on detailed morpho-anatomical observations as well as analyses of ITS and LSU nuclear rDNA. A key to the Capronia species present in Argentina is provided.
... dna extractIon, pcr amplIfIcatIon, and sequencIng Genomic DNA extraction from three weeks old cultures grown on MEA at 25°C together with PCR reactions to amplify the complete internal transcribed spacer (ITS) and partial nuclear ribosomal large subunit (LSU) regions along with a fragment of the translation elongation factor 1-alpha (EF1-α) gene were carried out separately for the Arizona and Czech isolates following the protocols outlined in Kirschner et al. (2013) and Koukol et al. (2018), respectively. In the case of strain MUCL 8886, DNA extraction and PCR amplification protocols were also performed separately for both the ITS-LSU and EF1-α regions based on Mardones et al. (2017) and Promputtha & Miller (2010), respectively. The primer pairs ITS1/ITS4 in combination with LR0R/LR5 (Vilgalys & Hester 1990;White et al. 1990) were used for PCR amplification and sequencing of the ITS-LSU regions of the Arizona isolate. ...
... The selected models using the Bayesian information criterion were TrN+I+G for both the LSU and EF1-α datasets of the septonema-like isolates, and TIM2ef+I+G, TrN+I+G and TrN+G for the ITS, LSU and EF1-α datasets of the MUCL strain, respectively. Phylogenetic relationships were reconstructed by Bayesian inference and Maximum likelihood (ML) approaches using MrBayes v.3.2 (Ronquist et al. 2012) and RAxML v.8.2.10 (Stamatakis 2014) on the CIPRES Science Gateway server (Miller et al. 2010), respectively. Two independent runs of 4-6 M generations were run for Bayesian analyses employing the GTRGAMMA model and sampling every 100th generation. ...
During independent surveys of microfungi associated with Pinus spp. in the United States and the Czech Republic, a distinct fungus matching the generic concept of Septonema Corda was collected. It is characterized by distinctly ornamented conidiophores, branches, conidia and hyphae, ranging from verruculose to strongly verrucose with prominent rounded warts, yellowish brown to brown or reddish brown in color and forming densely floccose, dark brown or dark reddish brown colonies on pine wood and bark. Conidia are cylindrical or subcylindrical and produced in short, simple or branched acropetal chains. Multigene phylogenetic analyses including nuclear ribosomal (LSU) and
protein coding gene (EF1-α) sequence data suggest that both collections are conspecific and belong to the order Mytilinidiales (Dothideomycetes, Ascomycota) where they group distant from other mytilinidiaceous fungi with known septonema-like anamorphs. To provide a proper name based on phylogenetic placement and to possibly circumscribe Septonema sensu stricto, a non-sporulating, putative strain belonging to S. secedens Corda, the generic type, was included in the analyses. DNA sequence data placed this strain within the family Venturiaceae (Venturiales, Dothideomycetes) but morphological examination of the corresponding herbarium specimen revealed that it belongs instead
to S. fasciculare (Corda) S. Hughes. Because of the polyphyletic nature of the genus and the unknown phylogenetic position of its type species, our fungus is accommodated in Septonema as a new species named S. lohmanii G. Delgado & Koukol, sp. nov.
... Newly generated sequences are in bold. Strains isolated from the holotype, epitype, paratype and reference specimens are indicated in with a red superscript H, E, P and R, respectively 257.59) , H. taiwanense (BCRC FU30841) (Kuo and Goh 2018a), Helicomyces bellus (CBS 113542) ) and Tubeufia aurantiella (ANM 718) (Promputtha and Miller 2010) under Neohelicosporium. We rename Helicomyces macrofilamentosus (HKUCC 10235) (Kodsueb et al. 2006) and H. torquatus (CBS 189.95) as Neohelicosporium sp. as they have been misidentified and available descriptions do not fit them into the generic concept of Neohelicosporium. ...
... Clade 25 (2 taxa) represents the new genus Acanthotubeufia. We synonymize Acanthostigma filiforme (ANM 101 and ANM 514) (Promputtha and Miller 2010) under Acanthotubeufia filiforme. ...
... Notes: This taxon was introduced as Acanthostigma filiforme by Promputtha and Miller (2010). Boonmee et al. (2014) synonymized it under Neoacanthostigma filiforme based on phylogenetic evidence. ...
This study deals with an extensive taxonomic reevaluation focusing on phylogenetic relationships and morphological characterization of Tubeufiales, especially those helicosporous hyphomycetes which are difficult to identify. Based on evidence from DNA sequence data and morphology, we introduce 13 new genera in the family Tubeufiaceae, viz. Acanthotubeufia, Dematiohelicoma, Dematiohelicomyces, Dematiohelicosporum, Dematiotubeufia, Helicoarctatus, Helicohyalinum, Helicotruncatum, Neochlamydotubeufia, Neohelicoma, Pleurohelicosporium, Pseudohelicomyces and Pseudohelicoon; transfer Chaetosphaerulina from Dothideomycetes genera incertae sedis, and Artocarpomyces and Helicodochium from Ascomycetes genera incertae sedis into Tubeufiaceae; introduce 52 new species, viz. Berkleasmium fusiforme, B. longisporum, Chlamydotubeufia cylindrica, Dematiohelicosporum guttulatum, Helicoarctatus aquaticus, Helicodochium aquaticum, Helicohyalinum infundibulum, Helicoma aquaticum, H. brunneisporum, H. cocois, H. rufum, H. fusiforme, H. longisporum, H. multiseptatum, H. rubriappendiculatum, H. septoconstrictum, H. tectonae, Helicomyces hyalosporus, Helicosporium aquaticum, H. flavisporum, H. setiferum, H. vesicarium, H. viridiflavum, Neochlamydotubeufia fusiformis, Neohelicomyces hyalosporus, Neohelicosporium acrogenisporum, N. astrictum, N. ellipsoideum, N. irregulare, N. krabiense, N. laxisporum, N. ovoideum, Pleurohelicosporium parvisporum, Pseudohelicomyces aquaticus, P. hyalosporus, Tubeufia abundata, T. bambusicola, T. brevis, T. brunnea, T. chlamydospora, T. dictyospora, T. eccentrica, T. fangchengensis, T. hechiensis, T. inaequalis, T. krabiensis, T. rubra, T. sessilis, T. sympodihylospora, T. sympodilaxispora, T. taiwanensis and T. tratensis; provide 43 new combinations, viz. Acanthohelicospora guianensis, Acanthotubeufia filiforme, Berkleasmium aquatica, B. guangxiense, B. latisporum, B. thailandicum, Dematiohelicoma perelegans, D. pulchrum, Dematiohelicomyces helicosporus, Dematiotubeufia chiangraiensis, Helicohyalinum aquaticum, Helicoma elinorae, H. gigasporum, H. hongkongense, H. linderi, H. nematosporum, H. pannosum, H. serpentinum, Helicomyces chiayiensis, Helicotruncatum palmigenum, Neochlamydotubeufia khunkornensis, Neohelicoma fagacearum, Neohelicomyces pallidus, Neohelicosporium abuense, N. aurantiellum, N. griseum, N. morganii, N. myrtacearum, N. nizamabadense, N. sympodiophorum, N. taiwanense, N. vesiculiferum, Pseudohelicomyces indicus, P. paludosus, P. talbotii, Pseudohelicoon gigantisporum, P. subglobosum, Tubeufia dentophora, T. geniculata, T. lilliputea, T. machaerinae, T. sympodiophora and T. xylophila; introduce 16 new records, viz. Dictyospora thailandica, Helicomyces colligatus, H. torquatus, Neohelicosporium guangxiense, N. hyalosporum, N. parvisporum, Thaxteriellopsis lignicola, Tubeufia aquatica, T. chiangmaiensis, T. cylindrothecia, T. filiformis, T. guangxiensis, T. laxispora, T. parvispora, T. roseohelicospora and T. tectonae. The taxonomy of Helicoma, Helicomyces and Helicosporium is revisited based on phylogenetic analyses and morphological evidence. Neorhamphoria is transferred to Bezerromycetaceae. Three species are excluded from the genus Chlamydotubeufia, twelve species from Helicoma, four species from Helicomyces, 25 species from Helicosporium, six species from Neoacanthostigma and one species from Tubeufia. A multi-gene phylogenetic tree based on maximum likelihood and Bayesian analyses of ITS, LSU, RPB2 and TEF1α sequence data of species of Tubeufiales is provided. Detailed descriptions and illustrations are provided, as well as the morphological comparison with similar taxa are explored. The checklist of accepted Tubeufiales species and re-organised Tubeufiales species are provided.
... dna extractIon, pcr amplIfIcatIon, and sequencIng Genomic DNA extraction from three weeks old cultures grown on MEA at 25°C together with PCR reactions to amplify the complete internal transcribed spacer (ITS) and partial nuclear ribosomal large subunit (LSU) regions along with a fragment of the translation elongation factor 1-alpha (EF1-α) gene were carried out separately for the Arizona and Czech isolates following the protocols outlined in Kirschner et al. (2013) and Koukol et al. (2018), respectively. In the case of strain MUCL 8886, DNA extraction and PCR amplification protocols were also performed separately for both the ITS-LSU and EF1-α regions based on Mardones et al. (2017) and Promputtha & Miller (2010), respectively. The primer pairs ITS1/ITS4 in combination with LR0R/LR5 (Vilgalys & Hester 1990;White et al. 1990) were used for PCR amplification and sequencing of the ITS-LSU regions of the Arizona isolate. ...
... The selected models using the Bayesian information criterion were TrN+I+G for both the LSU and EF1-α datasets of the septonema-like isolates, and TIM2ef+I+G, TrN+I+G and TrN+G for the ITS, LSU and EF1-α datasets of the MUCL strain, respectively. Phylogenetic relationships were reconstructed by Bayesian inference and Maximum likelihood (ML) approaches using MrBayes v.3.2 (Ronquist et al. 2012) and RAxML v.8.2.10 (Stamatakis 2014) on the CIPRES Science Gateway server (Miller et al. 2010), respectively. Two independent runs of 4-6 M generations were run for Bayesian analyses employing the GTRGAMMA model and sampling every 100th generation. ...
Fruiting bodies of the corticoid fungus Scytinostroma portentosum, known as mothball crust, have been sampled from a dead branch of sallow. Volatile organic compounds of the samples were extracted by means of liquid/liquid extraction and purified by solvent assisted flavour evaporation. In addition, solid-phase microextraction was applied on one fruiting body sample. The odour active compounds were identified by gas chromatography-mass spectrometry and olfactometry on two columns of different polarity and described by sensory detection. Furthermore, an aroma extract dilution analysis was performed to identify the main flavour compounds. The main odour compounds of S. portentosum with an FD factors ≥16 were 3-chloroindole responsible for the typical mothball odour, the mushroom odours oct-1-en-3-ol and oct-1-en-3-one, methyl p-anisate having an anise-like smell, the bloomy and sweet smelling terpenes linalool and nerolidol, as well as benzylacetone and methyl hexadecanoate. Herewith, a comprehensive aroma active volatilome of S. portentosum is presented.
... The regions that were compared were: (1) entire ITS region, (2) partial LSU, (3) the second largest subunit of the RNA polymerase II gene (rpb2), and (4) partial translation elongation factor 1-alpha (tef1). Sequences for these gene regions were obtained from GenBank for previously published Coniella species, while gene sequences for the holotype and three paratypes of the new species were Sanger sequenced according to Promputtha and Miller (2010) (Table 1). Individual gene alignments were conducted in SeaView v4.5.3 (Galtier et al. 1996) using Muscle v3.7 (Edgar 2004). ...
The draft genome, morphological description, and phylogenetic placement of Coniella lustricola sp. nov. (Schizoparmeaceae) are provided. The species was isolated from submerged detritus in a fen at Black Moshannon State Park, Pennsylvania, USA and differs from all other Coniella species by having ellipsoid to fusoid, inequilateral conidia that are rounded on one end and truncate or obtuse on the other end, with a length to width ratio of 2.8. The draft genome is 36.56 Mbp and consists of 870 contigs on 634 scaffolds (L50 = 0.14 Mb, N50 = 76 scaffolds), with 0.5% of the scaffold length in gaps. It contains 11,317 predicted gene models, including predicted genes for cellulose, hemicellulose, and xylan degradation, as well as predicted regions encoding for amylase, laccase, and tannase enzymes. Many members of the Schizoparmeaceae are plant pathogens of agricultural crops. This draft genome represents the first sequenced Coniella genome and will be a valuable tool for comparisons among pathogenic Coniella species.
... software/cap3). In the case of the ITS region the genomic DNA was extracted from a culture using a DNeasy® Mini Plant extraction kit (Qiagen Inc., Valencia, California) following the manufacturer's protocols and detailed methods used for PCR amplification and sequencing followed Promputtha & Miller (2010). ITS sequencing was then performed at the W.M.Keck Center at the University of Illinois Urbana-Champaign and the returned ITS sequences were assembled with Sequencher 5.1 (Gene Codes Corp, Ann Arbor, Michigan). ...
Taeniolella sabalicola sp. nov., isolated from a petiole of a dead leaf of Sabal palmetto collected in south Florida, U.S.A., is described and illustrated based on morphological, cultural and molecular data. The fungus is characterized by forming slowly growing, black, restricted colonies on culture media and effuse colonies with abundant aerial mycelium on natural substrate after incubation, semi-macronematous or micronematous, long, unbranched conidiophores and clavate, ellipsoidal or cylindrical, smooth or verruculose, brown to blackish brown, multiseptate conidia with transverse, longitudinal and oblique septa, often surrounded by a mucilaginous sheath and usually in simple or branched acropetal chains. Phylogenetic analyses based on partial nuclear ribosomal large subunit (LSU) and internal transcribed spacer (ITS) sequence data also suggest the fungus is distinct from other Taeniolella species and possess affinities with members of Sordariomycetidae (Ascomycota) but its ordinal or familial position within the subclass remains uncertain. Molecular data also confirm that Taeniolella sensu lato is polyphyletic and show that T. sabalicola is unrelated to the generic type, T. exilis, recently placed in the family Kirschsteiniotheliaceae within the class Dothideomycetes.
... The PCR reaction was carried out in 25 µL containing 3-5 µL template DNA, 2.5 µL BSA (New England BioLabs Inc, Ipswich, USA), 2.5 µL 50% DMSO (Sigma, St Louis, MO, USA), and 1 µL of each 10 µM forward (ITS5) and reverse (ITS4) primer (Promputtha & Miller, 2010). The rest of the volume was made up to 25 µL by adding molecular biology grade H 2 O (Fisher Scientific, Waltham, MA, USA). ...
One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.
