NOTE: Due to security issues, the ARSEF database search function is not currently available and we are transitioning to a site on the ARS-AZURE cloud. Please contact the curator (Kathryn.Bushley@usda.gov) if you need information about specific groups or a custom search of the database that can be sent via e-mail. Printed PDF catalogues of all isolates and other information about the collection are available on the ARSEF website at https://www.ars.usda.gov/northeast-area/ithaca-ny/robert-w-holley-center... The Agricultural Research Service Collection of Entomopathogenic Fungal Cultures is the world's largest, most kaleidoscopic, and most comprehensive collection of living cultures of fungi that are pathogenic to or associated with insects, spiders, mites, ticks, and other invertebrates. Some isolates in the collection are not themselves invertebrate pathogens but are critically important for the improvements of taxonomies and systematics for the many diverse groups of fungi represented here. As of July 2016, ARSEF maintains more than 13000 isolates of more than 700 taxa of fungi isolated from 1300 hosts collected at more than 2400 locations on every continent. The database is searchable by Fungi, Hosts, Locations, Provenance, or Accessions. Results are provided in PDF format. Catalog files are in the Adobe Acrobat (PDF) format and are readable with the Adobe Acrobat Reader. All catalogs and live searches of isolate data incorporate the most current supportable taxonomies for ARSEF fungi. Significant changes in the nomenclatural rules for many fungi have a large and ongoing impact on the entomopathogens in the order Hypocreales. These changes are discussed the introductory material in the catalogs. If you are unsure about the most current identifications for isolates, online searches of ARSEF accessions return taxonomic information in the collection database at the moment of the search.

The ARS Culture Collection is one of the largest public collections of microorganisms in the world, containing approximately 93,000 strains of bacteria and fungi. The collection is split into subcollections of molds, prokaryotes, and yeasts. In addition, the online catalog is searchable by genus, species, subvar type, and subspecies. The collection is housed within the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois. The scientists and staff of the ARS Culture Collection conduct and facilitate microbiological research that advances agricultural production, food safety, public health, and economic development. These goals are pursued through in-house research that improves understanding and utilization of microbiological diversity and through efforts to enhance the value and accessibility of microbial accessions in the Agricultural Research Service Culture Collection.

Boxwood plants are affected by many different diseases caused by fungi. Some boxwood diseases are deadly and quickly kill the infected plants, but with others, the plant can survive and even thrive when infected. The fungus that causes volutella blight is the most common of these weak boxwood pathogens. Even the healthiest boxwood plants are infected by the volutella fungus, and often there are no signs that the plants are hurt by the infection. In order to understand why the volutella blight fungus is such a weak pathogen and to understand the genetic mechanisms it uses to interact with boxwood, the complete genome of the volutella fungus was sequenced and characterized. These datasets are generated from the genome sequence of Pseudonectria foliicola, strain ATCC13545, the fungus responsible for volutella disease of boxwood. Datasets include the nuclear genome and mitochondrial genome assemblies (sequenced using Illumina technology), the predicted gene model dataset generated using MAKER, the multiple sequence alignment of single-copy orthologs used for phylogenetic analysis, CMAP files generated from SimpleSynteny analysis of mitogenomes, and high quality photographic images.

Organisms living in honey bees and honey bee colonies form large associative holobiont communities that are integral to bee biology. High-throughput sequencing approaches to characterize these holobiont communities from honey bees in various states of health and disease are now commonplace, producing large amounts of nucleotide sequence data that must be accurately and consistently analyzed in order to produce reliable and comparable reports. In addition, new species designations and revisions are actively being made from honey bee holobiont communities, complicating nomenclature in larger databases where taxonomic descriptions associated with archived sequences can quickly become outdated and misleading. To improve the accuracy and consistency of honey bee holobiont research, we have developed HoloBee: a curated database of publicly accessioned nucleotide sequences from the honey bee holobiont community. Except in rare and noted exceptions made by curators, sequences used in HoloBee were obtained from, or in association with, Apis mellifera (Western honey bee) as well as other honey bee species where available (e.g. Apis cerana, Apis dorsata, Apis laboriosa, Apis koschevnikovi, Apis florea, Apis andreniformis and Apis nigrocincta). Sources include: within or on the surface of honey bees (adult, pupae, larvae, egg), corbicular pollen, bee bread, royal jelly, honey, comb, hive surfaces (e.g. bottom board debris, frames, landing platforms), and isolates of microbes, parasites and pathogens from honey bees. HoloBee contains two non-overlapping sets of sequence data, HoloBee-Barcode and HoloBee-Mop, each of which have distinct intended uses. HoloBee-Barcode is a non-redundant database of taxonomically informative barcoding loci for all viruses, bacteria, fungi, protozoans and metazoans associated with honey bees (Apis spp.). It was created from an exhaustive master sequence archive of all valid holobiont sequences. Redundancy was removed from this master archive using a clustering algorithm that grouped sequences with ≥ 99% identity and retained the longest sequence from each cluster as the representative accession for that sequence type (“centroid”). These centroid sequences were concatenated into a fasta formatted file to create the HoloBee-Barcode database. Associated taxonomy for each centroid, including Superkingdom through Species and Strain/Isolate, was individually reviewed and corrected when necessary by a curator. Cross reference tables (separated according to 5 major taxonomic groups) provide a user-friendly outline of information for each centroid accession within HoloBee-Barcode including taxonomy, gene/product name, sequence length, the unaltered NCBI definition line, the number and identity of redundant sequences clustered within each centroid, and any additional information provided by the curator. HoloBee-Barcode centroid counts are: Viruses = 86; Bacteria = 496; Fungi = 41; Protozoa = 4; Metazoa = 60. HoloBee-Barcode is intended to improve and standardize quantitative and qualitative metagenomic descriptions of holobiont communities associated with honey bees by providing a curated set of barcode sequences. The goal of genetic barcoding is to associate a nucleotide sequence sample to a taxonomically valid species. Genomic regions targeted for such barcoding purposes varied by taxonomic group. The small subunit (SSU) ribosomal RNA, or 16S rRNA, is the most commonly used barcode for bacteria and is used in HB-Barcode. These 16S rRNA sequences will support the analysis of data generated with the widely used approach of amplicon-based 16S rRNA deep sequencing to study microbiota communities. Although barcode markers for fungi are less definitive than bacteria, HB-Barcode defaults to the ribosomal RNA internal transcribed spacer region (ITS), which typically includes ITS-1, 5.8S, and ITS-2. For some clades that cannot be resolved by this region, other barcode markers were selected. The majority of barcodes for metazoan taxa are the mitochondrial locus cytochrome c oxidase subunit I (COI). Complete mitochondrial DNA (mtDNA) sequence for Apis cerana (Asian honey bee) and Galleria mellonella (Greater wax moth) are included as barcodes for these species. We note that A. cerana mtDNA is included because it is considered a potentially invasive honey bee species and monitoring for its occurrence is in practice regionally, including in Australia, New Zealand and the USA. Protozoan barcodes include cytochrome b oxidase (Cytb), SSU, or ITS while entire genomes are used for viral barcoding. HoloBee-Mop is a database comprised mostly of chromosomal, mitochondrial and plasmid genome assemblies in order to aggregate as much honey bee holobiont genomic sequence information as possible. For a few organisms without genome assembly data, transcriptome data are included (e.g. Aethina tumida, small hive beetle). Unlike HoloBee-Barcode, redundancy removal was not performed on the HoloBee-Mop database and thus this resource provides an archive of nucleotide sequence assemblies from honey bee holobionts. However, since full viral genomes are used in HoloBee-Barcode, only redundant viral sequences occur in HoloBee-Mop. All accessions within each of these assemblies were concatenated into a single fasta formatted file to create the HoloBee-Mop database. The intended purpose of HoloBee-Mop is to improve honey bee genome and transcriptome assemblies by “mopping-up” as much viral, bacterial, fungal, protozoan and non-honey bee metazoan sequence data as possible. Therefore, sequence data remaining after processing reads through both HoloBee-Barcode and HoloBee-Mop that do not map to the honey bee genome may contain unique data from taxonomic variants or novel species. Details for each sequence assembly within HoloBee-Mop are tabulated in cross reference tables according to each major taxonomic group. HoloBee-Mop assembly counts are: Viruses = 2; Bacteria = 55; Fungi = 5; Protozoa = 1; Metazoa = 6. Follow the HoloBee database on Twitter at: https://twitter.com/HoloBee_db For questions about the HoloBee database, contact: HoloBee database team: holobee.db@gmail.com Jay Evans: Jay.Evans@ars.usda.gov Anna Childers: Anna.Childers@ars.usda.gov

The U.S. National Fungus Collections (BPI) are the “Smithsonian for fungi” and are the repository for over one million fungal specimens worldwide - the largest such collections in the world. The collection includes preserved organisms, their parts and products, and their associated data. Information associated with these specimens constitute an enormous data resource, especially about plant-associated fungi. The collections document fungi through time and space for the past 200 years. Data from the labels of more than 750,000 of the specimens have been entered into a database. These labels have information on the host on which the fungus was found and the locality in which the specimen was collected. Sixty percent of these specimens are from the United States and thus represent a large body of information about the fungi in this country. Data entry has been completed for the Uredinales (rusts), the Ustilaginales (smuts), the Polyporales (polypores), the Deuteromycetes (imperfect fungi), the Ascomycetes, and the C.G. Lloyd collections. Recent progress has been made in the computerization of specimens of the agarics and the "lower" fungi including the Oomycetes and Chytridiomycetes.