Conrad L. Schoch
A5059054710- Plant Pathogens and Fungal Diseases
- Mycorrhizal Fungi and Plant Interactions
- Yeasts and Rust Fungi Studies
- Lichen and fungal ecology
- Genomics and Phylogenetic Studies
- Fungal Biology and Applications
- Plant-Microbe Interactions and Immunity
- Microbial Community Ecology and Physiology
- Plant Pathogens and Resistance
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Protist diversity and phylogeny
- Genetic diversity and population structure
- Identification and Quantification in Food
- Plant Disease Resistance and Genetics
- Fungal and yeast genetics research
- Biomedical Text Mining and Ontologies
- Bacteriophages and microbial interactions
- Biofuel production and bioconversion
- Plant Diversity and Evolution
- Nematode management and characterization studies
- Plant and animal studies
- Essential Oils and Antimicrobial Activity
- Mycotoxins in Agriculture and Food
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
United States National Library of Medicine
2013
Oregon State University
2004-2011
University of Oregon
2006
Cornell University
2003
Plant (United States)
2003
Stellenbosch University
1999-2001
University of the Free State
1997
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). leverages data submitted to International Nucleotide Sequence Database Collaboration (INSDC) against combination computation, manual curation, collaboration produce standard set stable, non-redundant reference sequences. augments these sequences with current...
Six DNA regions were evaluated as potential barcodes for Fungi , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region mitochondrial cytochrome c oxidase subunit 1 used animal barcode was excluded marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from nuclear ribosomal RNA cistron compared together with three representative protein-coding genes (largest...
Abstract This revision of the classification eukaryotes, which updates that Adl et al. [ J. Eukaryot. Microbiol . 52 (2005) 399], retains an emphasis on protists and incorporates changes since 2005 have resolved nodes branches in phylogenetic trees. Whereas previous was successful re‐introducing name stability to classification, this provides a for lineages were then still unresolved. The supergroups withstood hypothesis testing with some modifications, but despite progress, problematic at...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published life science journals. Entrez system search retrieval operations most these data from 39 distinct databases. E-utilities serve as programming interface system. Augmenting many Web applications are custom implementations BLAST program optimized to specialized sets. New...
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass simple sugars that are converted chemical intermediates biofuels, such as ethanol. We assembled 89 scaffolds (sets ordered oriented contigs) generate 34 Mbp nearly contiguous T. genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering utility effectiveness carbohydrate-active enzymes reesei, its encodes fewer than any other sequenced fungus able hydrolyze...
Abstract This revision of the classification eukaryotes follows that Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved resolution many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling intervening years has massively increased genetic information at hand. Consequently, discovered novel clades, exciting new genera uncovered a massive species level...
Based on an overview of progress in molecular systematics the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships fungi. As part project "Assembling Fungal Tree Life" (AFTOL), results four Bayesian analyses are reported with complementary bootstrap assessment confidence based (1) a combined two-locus set (nucSSU and nucLSU rDNA)...
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum Fungi. This analysis is most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number superclass-level nodes that have previously evaded resolution and were unnamed in classifications Fungi are resolved for first time. Based on 6-gene we conducted phylogenetic informativeness 6 genes series ancestral character state reconstructions focused...
We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates 41 families (six newly described in this volume) Dothideomycetes.All currently accepted orders the class are represented first time addition to numerous previously unplaced lineages.Subclass Pleosporomycetidae is expanded include aquatic order Jahnulales.An ancestral reconstruction of basic nutritional modes supports transitions saprobic life histories plant associated...
The class Dothideomycetes is one of the largest groups fungi with a high level ecological diversity including many plant pathogens infecting broad range hosts. Here, we compare genome features 18 members this class, 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze structure, evolution, diverse strategies pathogenesis. most likely evolved from common ancestor more than 280 million years ago. sequences differ dramatically in size due variation repetitive content, but show much...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 38 distinct databases. E-utilities serve as programming interface system. Augmenting many web applications are custom implementations BLAST program optimized to specialized sets. New...
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that shared by animals fungi studied in due to their experimental tractability. pathogens or mutualists model systems analyse effector genes mechanisms diversification. In this study, we report the genome sequence phytopathogenic ascomycete Leptosphaeria maculans characterize its repertoire protein effectors. The L. has an unusual bipartite structure with alternating distinct...
We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted four loci (nuc SSU rDNA, nuc LSU TEF1, RPB2) for 96 taxa, representing five seven orders in current classification Dothideomycetes and several outgroup taxa representative major clades Pezizomycotina. resulting differentiated two main dothideomycete lineages comprising pseudoparaphysate Pleosporales aparaphysate Dothideales. propose subclasses Pleosporomycetidae (order Pleosporales)...
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate sequence data, tied to both correct taxonomic names and clearly annotated specimen has never been greater. Furthermore, growing number of molecular ecology microbiome projects using high-throughput sequencing require fast effective methods en masse assignments. In this article, we focus on selecting re-annotating a set marker reference...
Average nucleotide identity analysis is a useful tool to verify taxonomic identities in prokaryotic genomes, for both complete and draft assemblies. Using optimum threshold ranges appropriate different taxa, we have reviewed all genome assemblies GenBank with regard their identity. We present the methods used make such comparisons, current status of verifications, recent developments confirming species assignments new submissions.
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e....
The Capnodiales incorporates plant and human pathogens, endophytes, saprobes epiphytes, with a wide range of nutritional modes. Several species are lichenised, or occur as parasites on fungi, animals. aim the present study was to use DNA sequence data nuclear ribosomal small large subunit RNA genes test monophyly Capnodiales, resolve families within order. We designed primers allow amplification sequencing almost complete genes. Other than Capnodiaceae (sooty moulds), Davidiellaceae, which...
One hundred and five generic types of Pleosporales are described illustrated. A brief introduction detailed history with short notes on morphology, molecular phylogeny as well a general conclusion each genus provided. For those genera where the type or representative specimen is unavailable, note given. Altogether 174 treated. Phaeotrichaceae Krie-geriella, Zeuctomorpha Muroia excluded from Pleosporales. Based multigene phylogenetic analysis, suborder Massarineae emended to accommodate...
Pezizomycotina is the largest subphylum of Ascomycota and includes vast majority filamentous, ascoma-producing species. Here we report results from weighted parsimony, maximum likelihood Bayesian phylogenetic analyses five nuclear loci (SSU rDNA, LSU RPB1, RPB2 EF-1α) 191 taxa. Nine 10 classes currently recognized were represented in sampling. These data strongly supported monophyly Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes Sordariomycetes. Pezizomycetes Dothideomycetes...
Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections creating new risks for established ones. There is need rapid accurate identification of enable early diagnosis targeted antifungal therapy. Morphological biochemical methods time-consuming require trained experts. Alternatively, molecular methods, such as DNA barcoding, powerful easy tool monophasic identification, offer practical approach species less demanding in terms taxonomical expertise....
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz.Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae Pleosporaceae. In addition, two new introduced, i.e. Amniculicolaceae Lentitheciaceae. Pleomassariaceae treated as a synonym Melanommataceae, circumscriptions Lophiostomataceaes. str.,...