About
298
Publications
199,273
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
47,267
Citations
Introduction
Current institution
Additional affiliations
January 2009 - October 2021
Position
- Curator
Description
- Curator for fungi and team lead for NCBI Taxonomy
January 2003 - December 2008
December 1999 - March 2003
Publications
Publications (298)
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 us...
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fung...
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the...
The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This include...
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multina-tional, 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...
The NCBI Taxonomy resource (https://www.ncbi.nlm.nih.gov/taxonomy) has long been a trusted, curated hub for organism names, classifications, and links to related data for all taxonomic nodes. NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) is an improved way to leverage the rich data available at NCBI so users can effectively browse, search,...
Biodiversity genomics critically depends on correct taxonomic identification of the sample from which data are derived. Tracking of that taxonomic information through systems that archive data and report on genome sequencing efforts. For submission of data to the International Nucleotide Sequence Database Collaboration (INSDC) databases (DNA DataBa...
The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The...
Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curatin...
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verif...
Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered a...
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species. Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Sub...
Background
The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S l...
It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomencla...
Background: The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S...
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. Recent updates include new r...
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for a...
Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known a...
The RefSeq database at the National Center for Biotechnology Information (NCBI) contains curated versions of records in the public archive, GenBank. Targeted Loci BioProjects focuses on conserved single loci used in biodiversity studies and currently three Fungi projects, namely ITS, 18S and 28S are described in NCBI BioProject RefSeq databases. To...
More than 4000 Fungi assemblies are available from GenBank and its partners in the International Nucleotide Sequence Database Collaboration (INSDC), with many more expected. It is essential to verify their identity before selected as NCBI RefSeq genomes. Curators have been using gene and genome sequences from type material and a k-mer tree to revie...
The ITS RefSeq Targeted Loci (RTL) database for Fungi at NCBI currently contains high quality sequence records for more than 10,000 species. Since the first description of this project (Schoch et al., 2014) it has increased almost 4-fold and now contains ex-type sequences for 8 phyla, 51 classes, 181 orders and 2,231 genera. Complete ITS region cov...
This revision of the classification of eukaryotes follows that of Adl et al., 2012[J. Euk. Microbiol.59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted,environmental sampling in the intervening ye...
The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institut...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of t...
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening...
This is a representation of the current National Center for Biotechnology Information (NCBI) Taxonomy Database classification for Fungi to ordinal level (July 2018). It includes an incomplete selection of non-fungal names and fungal genera as examples
of specific curational actions.
Representation of reptile, amphibian and fish taxa in GenBank and allied INSDC databases continues to increase at a rapid pace. These sequences are among most valuable research products of ichthyology and herpetology collections and are integral to research in phylogenetics, evolution, ecology, medicine and conservation science. Yet many GenBank us...
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 for different prokaryotic taxa, we have reviewed all prokaryotic genome assemblies in GenBank with regard to their taxonomic identity. We present the methods...
The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institut...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank ® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of...
The combination of manual curation and the reliance on updates from submitters to the public sequence databases is currently inefficient and impedes the comprehensive and timely release of records with new taxonomic names. This should be improved by making several steps during data release more efficient. This article focuses on one such step by pr...
Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processi...
Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processi...
The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation ef...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of...
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits und...
The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity i...
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 (INSD...
Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming a...
Glyphium encompasses species with erect, carbonaceous ligulate to dolabrate ascomata that are strongly laterally compressed and dehisce along a longitudinal slit. The five currently recognized members of the genus are separated primarily by whether the ascospores disassociate into part-spores within the ascus. Glyphium has traditionally been placed...
The modern concepts of Dothideomycetes and Arthoniomycetes can be traced back to Luttrell (Mycologia 47:511–532, 1955) who, relying on data from a number of previous publications, combined lichenized and nonlichenized fungi in a single class, Loculoascomycetes. A current concept of two separate classes, as well-defined sister taxa, is still new, bu...
Background
Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Leptosphaeria maculans-Leptosphaeria biglobosa species complex (class Dothideomycetes, order Pleosporales), having different host...
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition o...
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 31...
MycoBank, a registration system for fungi established in 2004 to capture all taxonomic
novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and...
MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and...
Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS seque...
Count data for PCR amplification success (Positive) or failure (Negative), and post hoc test of results of Χ2 test of independence, for PCR success rate by taxon (genus) subdivided by decade of specimen collection (1980s–1990s vs. 2000s). Method for calculation of standardized and adjusted residuals (STARs) is cited in the main article. Significant...
UPGMA dendrogram showing clustering of 1107 ITS sequences obtained from vouchered macrofungal collections in the herbarium of the Venice natural history museum. Columns to the right of the taxon names indicate clustering by genus and family, facilitating identification of misidentified specimens or taxonomic issues.
(JPG)
UPGMA dendrogram showing clustering of ITS sequences, containing only those species for which multiple accessions were sequenced. Non-identical sequences for multiple accessions of a species indicate possible instances of misidentification, intraspecific polymorphism, or cryptic species. Columns to the right of the taxon names indicate clustering b...
Collection data.
(XLSX)
