Author
Dominik Begerow
Other affiliations: Max Planck Society, University of Tübingen
Bio: Dominik Begerow is an academic researcher from Ruhr University Bochum. The author has contributed to research in topics: Ustilaginomycotina & Microbotryum. The author has an hindex of 39, co-authored 120 publications receiving 10397 citations. Previous affiliations of Dominik Begerow include Max Planck Society & University of Tübingen.
Topics: Ustilaginomycotina, Microbotryum, Biology, Genus, Ustilaginomycetes
Papers published on a yearly basis
Papers
More filters
Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: 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.
Abstract: 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.
4,116 citations
Clark University1, National Institutes of Health2, Louisiana State University3, CABI4, Umeå University5, Field Museum of Natural History6, Duke University7, University of Minnesota8, University of Alabama9, Oregon State University10, Centraalbureau voor Schimmelcultures11, United States Department of Agriculture12, University of Tübingen13, Max Planck Society14, University of Florida15, Pennsylvania State University16, Aberystwyth University17, Complutense University of Madrid18, University of Oslo19, University of Hong Kong20, University of Tartu21, University of Gothenburg22, University of Kansas23, University of Maine24, University of Illinois at Urbana–Champaign25, Royal Ontario Museum26, Georgia State University27, Estonian University of Life Sciences28, Washington State University29, Nova Southeastern University30, Ludwig Maximilian University of Munich31, University of Western Ontario32, Uppsala University33, Brandon University34, Royal Botanic Garden Edinburgh35, State University of New York at Purchase36, Boise State University37, Cornell University38
TL;DR: A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community.
2,096 citations
Agriculture and Agri-Food Canada1, University of Sydney2, Institut national de la recherche agronomique3, Aix-Marseille University4, university of lille5, University of Amsterdam6, American Museum of Natural History7, Leibniz Association8, Ruhr University Bochum9, Universidade Nova de Lisboa10, Federal University of Paraná11, Agro ParisTech12, University of Perugia13, Tuscia University14, Pasteur Institute15, Spanish National Research Council16, Second Military Medical University17, University of Pretoria18, King Abdulaziz University19, Staatliches Museum für Naturkunde Stuttgart20
TL;DR: A novel high fidelity primer pair for TEF1α has potential as a supplementary DNA barcode with superior resolution to ITS, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Abstract: Primer development and testing by partners in the
European Consortium of Microbial Resource Centres (EMbaRC) was supported
through funding of the European Community’s Seventh Framework
Programme (FP7, 2007–2013), Research Infrastructures action, under grant
agreement no. FP7-228310. Part of sequencing work in CBS was supported
by Fonds Economische Structuurversterking (FES), Dutch Ministry of Education,
Culture and Science grant BEK/BPR-2009/137964-U). WM and VR
were supported by research grant NH&MRC #APP1031952. Genome mining
at CBS and AAFC, and primer development and testing at AAFC, were supported
by grants from the A.P. Sloan Foundation Programme on the Microbiology
of the Built Environment. We acknowledge the Deanship of Scientific
Research (DSR), King Abdulaziz University, under grant No. 1-965/1434 HiCi
for technical and financial support. AY was supported by Fundacao para a
Ciencia e a Tecnologia (Portugal), project PTDC/BIA-BIC/4585/2012. MPM
was supported by grant CGL2012-359 (Spain).
385 citations
TL;DR: It is demonstrated that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.
Abstract: Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists
364 citations
Complutense University of Madrid1, Natural History Museum2, Centraalbureau voor Schimmelcultures3, University of California, Berkeley4, University of Pretoria5, Ege University6, Louisiana State University7, Trakya University8, Ruhr University Bochum9, Anadolu University10, Landcare Research11, Murdoch University12, Medical University of Graz13, Royal Botanic Gardens14, University of Sydney15, Université catholique de Louvain16, Vienna University of Technology17, University of Nottingham18, University of Miami19, Technical University of Denmark20, Pennsylvania State University21, Leiden University22, Federal University of Paraná23, Canadian Grain Commission24, Wageningen University and Research Centre25, Clark University26, National Academy of Agricultural Sciences27, Field Museum of Natural History28, Istanbul University29, CABI30, University of Tartu31, United States Department of Agriculture32, University of Illinois at Urbana–Champaign33, Mashhad University of Medical Sciences34, Russian Academy of Sciences35, Swedish University of Agricultural Sciences36, Celal Bayar University37, Goethe University Frankfurt38, University of Szeged39, University of Antioquia40
TL;DR: The Amsterdam Declaration on Fungal Nomenclature 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.
Abstract: 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.
328 citations
Cited by
More filters
Journal Article•
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Abstract: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
7,032 citations
Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: 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.
Abstract: 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.
4,116 citations
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations
American Museum of Natural History1, University of Tartu2, University of Gothenburg3, James Hutton Institute4, University of Aberdeen5, Cooperative Institute for Research in Environmental Sciences6, University of California, Berkeley7, Aberystwyth University8, Estonian University of Life Sciences9, Spanish National Research Council10, Royal Botanic Gardens11, Academy of Sciences of the Czech Republic12, Swedish University of Agricultural Sciences13, University of Tennessee14, University of Helsinki15, Stanford University16, Ludwig Maximilian University of Munich17, University of Toronto18, University of Florida19, University of New Mexico20, University of Tübingen21
TL;DR: All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type, and the term ‘species hypothesis’ (SH) is introduced for the taxa discovered in clustering on different similarity thresholds.
Abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
2,605 citations