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Find video protocols related to scientific articles indexed in Pubmed.
Diversity of Penicillium section Citrina within the fynbos biome of South Africa, including a new species from a Protea repens infructescence.
Mycologia
PUBLISHED: 05-28-2014
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During a survey of the fynbos biome in the Western Cape of South Africa, 61 Penicillium species were isolated and nine belong to Penicillium section Citrina. Based on morphology and multigene phylogenies, section Citrina species were identified as P. cairnsense, P. citrinum, P. pancosmium, P. pasqualense, P. sanguifluum, P. sizovae, P. sumatrense and P. ubiquetum. One of the species displayed unique phenotypic characters and DNA sequences and is described here as P. sucrivorum. Multigene phylogenies consistently resolved the new species in a clade with P. aurantiacobrunneum, P. cairnsense, P. miczynksii, P. neomiczynskii and P. quebecense. However, ITS, ?-tubulin and calmodulin gene sequences are unique for P. sucrivorum and growth rates on various media, the ability to grow at 30 C, a positive Ehrlich reaction and the absence of sclerotia on all media examined, distinguish P. sucrivorum from all of its close relatives.
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Recommendations on generic names competing for use in Leotiomycetes (Ascomycota).
IMA Fungus
PUBLISHED: 05-23-2014
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In advancing to one scientific name for fungi, this paper treats genera competing for use in the phylogenetically defined class Leotiomycetes except for genera of Erysiphales. Two groups traditionally included in the so-called "inoperculate discomycetes" have been excluded from this class and are also not included here, specifically Geoglossomycetes and Orbiliomycetes. A recommendation is made about the generic name to use in cases in which two or more generic names are synonyms or taxonomically congruent along with the rationale for the recommendation. In some cases the recommended generic name does not have priority or is based on an asexual type species, thus needs to be protected and ultimately approved according to Art. 57.2 of the International Code of Nomenclature for algae, fungi and plants (ICN). A table is presented listing all competing generic names and their type species noting the recommended generic name. New combinations are introduced for the oldest epithet in the recommended genus including Ascocalyx berenice, Ascoconidium purpurascens, Ascocoryne albida, A. trichophora, Blumeriella filipendulae, B. ceanothi, Botrytis arachidis, B. fritillariae-pallidoflori, Calloria urticae, Calycellina aspera, Dematioscypha delicata, Dermea abietinum, D. boycei, D. stellata, Diplocarpon alpestre, D. fragariae, Godroniopsis peckii, Grovesinia moricola, Heterosphaera sublineolata, Hyphodiscus brachyconium, H. brevicollaris, H. luxurians, Leptotrochila campanulae, Monilinia polystroma, Neofabraea actinidae, N. citricarpa, N. vagabunda, Oculimacula aestiva, O. anguioides, Pezicula brunnea, P. californiae, P. cornina, P. diversispora, P. ericae, P. melanogena, P. querciphila, P. radicicola, P. rhizophila, Phialocephala piceae, Pilidium lythri, Rhabdocline laricis, Streptotinia streptothrix, Symphyosirinia parasitica, S. rosea, Unguiculariopsis caespitosa, and Vibrissea laxa.
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.
Conrad L Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, László Irinyi, Wieland Meyer, R Henrik Nilsson, Karen Hughes, Andrew N Miller, Paul M Kirk, Kessy Abarenkov, M Catherine Aime, Hiran A Ariyawansa, Martin Bidartondo, Teun Boekhout, Bart Buyck, Qing Cai, Jie Chen, Ana Crespo, Pedro W Crous, Ulrike Damm, Z Wilhelm De Beer, Bryn T M Dentinger, Pradeep K Divakar, Margarita Dueñas, Nicolas Feau, Katerina Fliegerová, Miguel A García, Zai-Wei Ge, Gareth W Griffith, Johannes Z Groenewald, Marizeth Groenewald, Martin Grube, Marieka Gryzenhout, Cécile Gueidan, Liangdong Guo, Sarah Hambleton, Richard Hamelin, Karen Hansen, Valérie Hofstetter, Seung-Beom Hong, Jos Houbraken, Kevin D Hyde, Patrik Inderbitzin, Peter R Johnston, Samantha C Karunarathna, Urmas Kõljalg, Gábor M Kovács, Ekaphan Kraichak, Krisztina Krizsán, Cletus P Kurtzman, Karl-Henrik Larsson, Steven Leavitt, Peter M Letcher, Kare Liimatainen, Jian-Kui Liu, D Jean Lodge, Janet Jennifer Luangsa-ard, H Thorsten Lumbsch, Sajeewa S N Maharachchikumbura, Dimuthu Manamgoda, María P Martín, Andrew M Minnis, Jean-Marc Moncalvo, Giuseppina Mulè, Karen K Nakasone, Tuula Niskanen, Ibai Olariaga, Tamás Papp, Tamás Petkovits, Raquel Pino-Bodas, Martha J Powell, Huzefa A Raja, Dirk Redecker, J M Sarmiento-Ramirez, Keith A Seifert, Bhushan Shrestha, Soili Stenroos, Benjamin Stielow, Sung-Oui Suh, Kazuaki Tanaka, Leho Tedersoo, M Teresa Telleria, Dhanushka Udayanga, Wendy A Untereiner, Javier Diéguez Uribeondo, Krishna V Subbarao, Csaba Vágvölgyi, Cobus Visagie, Kerstin Voigt, Donald M Walker, Bevan S Weir, Michael Weiss, Nalin N Wijayawardene, Michael J Wingfield, J P Xu, Zhu L Yang, Ning Zhang, Wen-Ying Zhuang, Scott Federhen.
Database (Oxford)
PUBLISHED: 01-01-2014
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DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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Basidioascus and Geminibasidium: a new lineage of heat-resistant and xerotolerant basidiomycetes.
Mycologia
PUBLISHED: 05-25-2013
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Using a heat-treatment method, two genera of heat-resistant and xerotolerant basidiomycetes were isolated from soil samples. These two genera, Basidioascus and Geminibasidium gen. nov., are morphologically similar and phylogenetically related. The genus Basidioascus originally was described as an ascomycete, but the structures originally interpreted as single-spored asci appear to represent basidiospores. Morphologically both genera are characterized by the lack of a fruiting body, conspicuously granular and deciduous basidia with a unique basal lateral projection and apparently double-walled basidiospores. The basidia, rather than the basidiospores, are forcibly discharged in Basidioascus species but not in Geminibasidium species. In Geminibasidium species a putative basidium arises from a primary cell. These are novel forms of basidia ontogenesis previously unseen in basidiomycetes. The rDNA (SSU + 5.8S + LSU) Bayesian phylogenetic analysis suggests that these fungi are distantly related to Wallemia, another xerotolerant basidiomycete genus commonly found in indoor air dust, dried foods and natural hypersaline environments. Given the physiological similarity and phylogenetic relationships, Basidioascus and Geminibasidium are classified in a new order, Geminibasidiales, and are taxonomically assigned to the class Wallemiomycetes. Based on morphological observations and molecular phylogeny of the internal transcribed spacer (ITS), two species of Basidioascus (B. undulatus, B. magus sp. nov.) and two species of Geminibasidium (G. donsium sp. nov., G. hirsutum sp. nov.) are described. A key to these species is provided using micromorphological and cultural characters.
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Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection.
IMA Fungus
PUBLISHED: 03-23-2013
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With the recent changes concerning pleomorphic fungi in the new International Code of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae, Clonostachys is recommended over Bionectria; in Hypocreaceae, Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae, Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.
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The amsterdam declaration on fungal nomenclature.
IMA Fungus
PUBLISHED: 05-17-2011
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The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
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Quantifying microbial communities with 454 pyrosequencing: does read abundance count?
Mol. Ecol.
PUBLISHED: 11-03-2010
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Pyrosequencing technologies have revolutionized how we describe and compare complex microbial communities. In 454 pyrosequencing data sets, the abundance of reads pertaining to taxa or phylotypes is commonly interpreted as a measure of genic or taxon abundance, useful for quantitative comparisons of community similarity. Potentially systematic biases inherent in sample processing, amplification and sequencing, however, may alter read abundance and reduce the utility of quantitative metrics. Here, we examine the relationship between read abundance and biological abundance in a sample of house dust spiked with known quantities and identities of fungi along a dilution gradient. Our results show one order of magnitude differences in read abundance among species. Precision of quantification within species along the dilution gradient varied from R(2) of 0.96-0.54. Read-quality based processing stringency profoundly affected the abundance of one species containing long homopolymers in a read orientation-biased manner. Order-level composition of background environmental fungal communities determined from pyrosequencing data was comparable with that derived from cloning and Sanger sequencing and was not biased by read orientation. We conclude that read abundance is approximately quantitative within species, but between-species comparisons can be biased by innate sequence structure. Our results showed a trade off between sequence quality stringency and quantification. Careful consideration of sequence processing methods and community analyses are warranted when testing hypotheses using read abundance data.
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How to describe a new fungal species.
IMA Fungus
PUBLISHED: 10-09-2010
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The formal requirements and best practices for the publication of descriptions of new fungal species are discussed. Expectations for DNA sequences and cultures are considered. A model manuscript offers one possible approach to writing such a paper.
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Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-28-2010
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Fungi are ubiquitous components of indoor human environments, where most contact between humans and microbes occurs. The majority of these organisms apparently play a neutral role, but some are detrimental to human lifestyles and health. Recent studies that used culture-independent sampling methods demonstrated a high diversity of indoor fungi distinct from that of outdoor environments. Others have shown temporal fluctuations of fungal assemblages in human environments and modest correlations with human activity, but global-scale patterns have not been examined, despite the manifest significance of biogeography in other microbial systems. Here we present a global survey of fungi from indoor environments (n = 72), using both taxonomic and phylogeny-informative molecular markers to determine whether global or local indoor factors determine indoor fungal composition. Contrary to common ecological patterns, we show that fungal diversity is significantly higher in temperate zones than in the tropics, with distance from the equator being the best predictor of phylogenetic community similarity. Fungal composition is significantly auto-correlated at the national and hemispheric spatial scales. Remarkably, building function has no significant effect on indoor fungal composition, despite stark contrasts between architecture and materials of some buildings in close proximity. Distribution of individual taxa is significantly range- and latitude-limited compared with a null model of randomized distribution. Our results suggest that factors driving fungal composition are primarily global rather than mediated by building design or function.
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Development of a specific TaqMan real-time PCR assay for quantification of Fusarium graminearum clade 7 and comparison of fungal biomass determined by PCR with deoxynivalenol content in wheat and barley.
Int. J. Food Microbiol.
PUBLISHED: 03-12-2010
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A Fusarium graminearum clade 7 specific real-time quantitative PCR (qPCR) assay was developed in this study based on unique polymorphisms in sequences of the mating type protein (MAT) gene. PCR amplification was not observed in eight phylogenetic lineages of the F. graminearum complex and four other closely related Fusarium species. Accuracy of the quantification of the real-time PCR assay was verified with wheat DNA spiked with F. graminearum clade 7 DNA. Wheat samples representing two Canadian wheat classes, CWRS (Canadian Western Red Spring) and CWRW (Canadian Western Red Winter) were used to determine the relationships among F. graminearum DNA, deoxynivalenol (DON) and Fusarium damaged kernel (FDK). The amount of DON and F. graminearum DNA remaining after removal of FDK varied among samples, but was sometimes substantial. Positive correlations were observed between F. graminearum clade 7 DNA (in picograms) and DON as well as FDK. There was also a strong correlation between FDK and DON in CWRS and CWRW wheat composite samples, but the inherent variability in individual producer samples precluded a definitive correlation. For barley, a positive correlation was observed between Fusarium DNA and DON values. Real-time PCR assays can be a valuable tool for barley as there are no reliable symptoms to visually assess the level of Fusarium head blight in this crop.
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Contamination with storage fungi of human food from Cameroon.
Int. J. Food Microbiol.
PUBLISHED: 07-02-2009
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In a mycological study, a total of 95 human food samples were investigated to evaluate the incidence of fungal contamination in Cameroon by conventional identification method and partly confirmed by DNA sequencing. The isolated fungal spp. were further studied to determine their toxigenic potentials. The investigation revealed the predominance of Aspergillus and Penicillium with 96% of samples contaminated with at least one species of these fungi, whereas the incidence of co-contamination of samples was 85%. Aspergillus flavus and Aspergillus parasiticus (Flavi section) were the most predominant species contaminating mainly maize and peanuts. In addition, P. crustosum and P. polonicum were the most common contaminants belonging to the genus Penicillium. On the other hand, A. ochraceus (Circumdati section) registered a low incidence rate of 5%, including other members of the Aspergillus group. Other members of the genera Rhizopus and Alternaria spp. were also registered in the study. A majority of fungal strains of A. ochraceus, A. parasiticus, P. crustosum and P. polonicum isolated were toxigenic, producing the mycotoxins tested for, while none was detected in cultures of A. fumigatus. The high incidence rate of fungi contamination coupled with their potentials in producing mycotoxins gives a strong indication that the samples tested may likely be contaminated with various mycotoxins. There is need for further study to assess the incidence of mycotoxins contamination in similar food samples.
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Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium.
Mol Ecol Resour
PUBLISHED: 05-01-2009
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Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1-based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences.
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Progress towards DNA barcoding of fungi.
Mol Ecol Resour
PUBLISHED: 05-01-2009
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The use of DNA sequences for identifying fungi and fungus-like organisms predates the DNA barcoding movement by at least 10 years. A brief overview of the mycological shift from phenotypic to molecular taxonomy is provided. Exploration of the animal barcode marker, cytochrome oxidase 1, by Canadian mycologists has been fruitful for some fungi, but intron issues and lack of resolution in other taxa prevent its universal application. The momentum established by 15 years of research on the fungal nuclear ribosomal internal transcribed spacer (ITS) sequences will lead to a proposal to the Consortium for the Barcode of Life on the adoption of this marker as the fungal barcode. Existing mycological research networks should facilitate the rapid development of DNA barcoding of fungi once the marker issue is settled. Some available online fungal identification databases are briefly described.
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Description of Cryptosporiopsis kienholzii and species profiles of Neofabraea in major pome fruit growing districts in the Pacific Northwest USA.
Mycol. Res.
PUBLISHED: 04-06-2009
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The objectives of this study were i) to give a taxonomic description of a fungus phylogenetically related to Neofabraea and assign the name Cryptosporiopsis kienholzii to this fungus, ii) to expand previous Neofabraea species profiles from infected apple and pear fruit collected from major pome fruit production districts in Oregon and Washington, and iii) to determine the sensitivity of Neofabraea alba, Neofabraea malicorticis, Neofabraea perennans, and C. kienholzii to a range of fungicides. A name is given herein to the anamorph of the fungus previously called Neofabraea sp. nov. in the literature, and the fungus is designated as C. kienholzii. The teleomorph of this fungus has never been observed in vivo or in vitro. N. alba, N. perennans, and C. kienholzii accounted for 61.3, 35.6, and 3.1 %, respectively, of 608 isolates obtained from pear fruit and 6.0, 81.3, and 12.7 % of 150 isolates from apple fruit. N. alba was the most common species in Oregon and N. perennans was most common in Washington. N. malicorticis was not found in any of the districts and may be limited to the wet climates west of the Cascade mountain range. C. kienholzii occurs in pome fruit orchards from southern Oregon to North Central Washington, and this is the first report of C. kienholzii in the state of Washington. The four most effective fungicides for control of bulls-eye rot caused by all species were thiabendazole, thiophanate-methyl, pyrimethanil, and pyraclostrobin+boscalid. Other fungicides gave acceptable control of some species of Neofabraea but not others. There was good agreement of the microbioassay with fungicide evaluations using wound-inoculated pear fruit for five of seven fungicides, but the microbioassay was not consistent enough for determination of the sensitivity of Neofabraea species to new fungicides.
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Phylogenetic classification of Pleurothecium and Pleurotheciella gen. nov. and its dactylaria-like anamorph (Sordariomycetes) based on nuclear ribosomal and protein-coding genes.
Mycologia
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Two strains of an unidentified perithecial ascomycete with a dactylaria-like anamorph and another morphologically similar strain of a dactylaria-like fungus were collected on decaying wood submerged in freshwater. To study their phylogenetic relationships we (i) combined sequence data from the nuclear small and large subunits ribosomal DNA (nc18S and nc28S) and the second largest subunit of RNA polymerase II (RPB2) for a multigene phylogenetic analysis and (ii) used sequences of the internal transcribed spacer region (ITS) of the rRNA operon for a species-level analysis. The new genus Pleurotheciella is described for two new species, Pla. rivularia and Pla. centenaria, with nonstromatic perithecia, unitunicate asci, persistent paraphyses and hyaline, septate ascospores and dactylaria-like anamorphs characterized by holoblastic, denticulate conidiogenesis, subhyaline conidiophores and hyaline, septate conidia. Based on morphological and molecular data, Pleurotheciella is closely related to the genera Pleurothecium and Sterigmatobotrys. A key to the three genera and the known species is provided. In the three-gene inferred phylogeny, these genera grouped as a sister clade to the Savoryellales within a robust clade of uncertain higher rank affiliation. Phylogenetic study of the 12 strains that represent Pleurothecium recurvatum revealed four that grouped apart from the core of the species. Two of these strains, which form a monophyletic well supported clade in both phylogenies and share similar morphological characteristics, are described as a new species, Pleurothecium semifecundum.
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Cirrosporium novae-zelandiae, an enigmatic coelomycete with meristem arthroconidia, with ancestors in the Eurotiomycetes.
Mycologia
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A culture of Cirrosporium novae-zelandiae, the type species of a distinctive, monotypic coelomycete genus, was isolated from a specimen collected near the holotype locality in New Zealand. Light microscopic and environmental scanning electron microscopic observations confirm the details of the unusual meristem arthric conidium ontogeny presented in the protolog. For phylogenetic analysis, a dataset of 122 species representing nine classes of euascomycetes was assembled including sequences from nuclear small and large subunits (nc18S, nc28S) and mitochondrial small subunit (mr16S) ribosomal RNA and the largest and second largest subunits of RNA polymerase II (RPB1, RPB2). A five-gene phylogeny suggests that the fungus is phylogenetically related to the Eurotiomycetes. It sits alone on a long branch as a sister to the Mycocaliciales of the Mycocaliciomycetidae. Cirrosporium exhibits several morphological characters similar to those of members of the Mycocaliciales; however, the paucity of known anamorphs in this order does not offer any further clarification on possible relationships. It is clear that the rare and broadly distributed meristem arthric ontogenetic pattern is polyphyletic, occurring in widely separate groups of anamorphs of both the Ascomycota and Basidiomycota.
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Proc. Natl. Acad. Sci. U.S.A.
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Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.