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.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Alfred P. Sloan Foundation [G-2015-14062]; Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning [FORMAS, 215-2011-498]; European Regional Development Fund (Centre of Excellence EcolChange) [TK131]; Estonian Research Council [IUT20-30]. Funding for open access charge: Swedish Research Council of Environment, Agricultural Sciences and Spatial Planning.

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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

BACKGROUND: Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential. METHODS: To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups' findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved. RESULTS: There is no change in the classifications of "proven," "probable," and "possible" IFD, although the definition of "probable" has been expanded and the scope of the category "possible" has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses. CONCLUSIONS: These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.

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Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium

Fungal diseases represent an important paradigm in immunology, as they can result from either a lack of recognition by the immune system or overactivation of the inflammatory response. Research in this field is entering an exciting period of transition from studying the molecular and cellular bases of fungal virulence to determining the cellular and molecular mechanisms that maintain immune homeostasis with fungi. The fine line between these two research areas is central to our understanding of tissue homeostasis and its possible breakdown in fungal infections and diseases. Recent insights into immune responses to fungi suggest that functionally distinct mechanisms have evolved to achieve optimal host-fungus interactions in mammals.

Immunity to Fungal Infections

The atlas compiled by these editors is a commendable effort and welcome addition to the mycology textbook sector. Up until now, the publication of medical mycology textbooks has been sparse and those that have been published are either too detailed for a resident in training or practicing physician or do not provide sufficient photographs or illustrations of the main features of the mycotic organisms. As a lecturer in mycology for the dermatology residents at my local teaching hospital and program, there are 3 key objectives of my mycology lectures: (1) to provide some type of organizational approach to mycotic organisms, (2) to provide a concise clinical history, and (3) to provide as many photographs and illustrations of mycotic organisms as possible. This atlas provides an exemplary addition to my book collection on medical mycology textbooks and sources for illustrations of mycotic organisms. The electron photomicrographs, photoplates, and line drawings of

Atlas of Clinical Fungi

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Studies of evolutionary relationships of Phoma species based on phylogenetic markers

Botrytis cinerea causes the gray molds or gray mold of fruits and vegetables, both in the field and in storage. Almost all fresh fruits, vegetables, and bulbs are attacked by B. cinerea in storage (Agrios, 1997). In wine production, their most serious damage is qualitative, from the modified chemical composition of diseased berries. The fungus converts simple sugar (glucose and fructose) to glycerol and gluconic acid and produces enzymes that catalyze the oxidation of phenolic compounds. It also secretes polysaccharides such as -glucan, which hinder the clarification of wine. Wine produced from rotten grape fruits has off-flavors and is fragile and sensitive to oxidation and bacterial contamination, making them unsuitable for aging (Jarvis, 1977, McClellan and Hewitt, 1973). The use of synthetic chemicals to control plant diseases is restricted due to their possible carcinogenicity, acute toxicity, long degradation periods, environmental pollution and their effects on human beings (Lingk, 1991). Therefore alternative to synthetic pesticides are needed from microbial and plant sources. Effective phytocompounds are expected to be far more advantageous than synthetic pesticides, as they are easily decomposable, not environmental pollutants and posses no residual or phytotoxic properties (Tewari, 1990, Rao, 1990, Badei et al., 1996, Bishop and Thornton, 1997). The importance of spices and their derivatives (extracts, essential oils, decoctions, hydrosols) in crop protection is being increasingly recognized under the concept of Integrated Pest and Disease Management (IPDM). Under this concept, all possible modes of plant pests and disease control methods should be integrated to minimize the excessive use of synthetic pesticides (Beg and Ahmed, 2002). During the last years there has been growing interest in testing natural compunds of different origins as defense for cultivated plants against phytopathogenic fungi (Thompson, 1989, Kishore et al., 1989, Tewari, 1995, Muller-Riebau et al., 1995, Wilson et al., 1997, Bowers and Locke,

Effect of ground material of certain plant species against Botrytis cinerea.

Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.

Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections

Molecular Mycology ResearchLaboratory, Centre for InfectiousDiseases and Microbiology, SydneyMedicalSchool–WestmeadHospitalMarie Bashir Institute for InfectiousDiseases and BiosecurityThe University of SydneyWestmead Millennium Institute176 Hawkesbury Road, WestmeadSydney, NSW 2145, AustraliaTel: +61 2 8627 3430Fax: +61 2 9891 5317Email: wieland.meyer@sydney.edu.au

Laszlo Irinyi

Papers

Studies of evolutionary relationships of Phoma species based on phylogenetic markers

Effect of ground material of certain plant species against Botrytis cinerea.

Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections

DNA barcoding of human and animal pathogenic fungi: the ISHAM-ITS database

In silico environmental sampling of emerging fungal pathogens via big data analysis