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

Phoma is a genus containing more than 2000 described species. This genus traditionally refers to simple stem inhabiting pycnidial fungus with small hyaline, unicellular pycnidiospores (Sutton, 1980). Phomas cause various serious diseases to plants as well as to humans (Rai 1989, 2000). Besides these harmful aspects, certain Phoma species also contains antibiotic potential and economically useful secondary metabolites. As widespread plant pathogens around the world occur on a broad range of plant species, e.g. P. glomerata has been reported on grape, potato, wheat, pear, mango, rice and many other crops. Some important example include Phoma lingam that causes the very serious blackleg disease in canola. It is also found on other cruciferous crops such as cabbages, cauliflower and summer rape. P. medicaginis var. medicaginis is the causal agent of spring black stem of alfalfa. P. pinodella causes foot rot in peas and black stem in clovers. All of these pathogens can overwinter in crop debris and are often seedborne. Development of disease symptoms caused by these Phoma spp. will often be enhanced in wet and cool conditions. Within this genus large pathogenic variations are shown which often complicates the control of Phoma, especially in legumes.

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Phomas - can these fungi be used as biocontrol agents and sources of secondary metabolites? (A review).

The ascomycetous fungus Cryphonectria parasitica (Murr.) is one of the most important fungal pathogens of chestnut (Castanea sativa Mill.), causing chestnut blight. It is originated from Eastern Asia and was introduced into North America, and later into Europe. Almost 100 C. parasitica isolates were collected mainly from the Carpathian Basin to study their diversity and phylogenetic relationships. Three nuclear molecular markers were tested: (i) internal transcribed spacers (ITS), (ii) translation elongation factor 1 subunit alpha (tef1), and (iii) six microsatellite loci. The ITS region proved to be highly polymorphic but this kind of variability did not reflect the geographical regions of the isolates, while the tef1 sequences were identical in all isolates. Microsatellite haplotype diversity was relatively high (0.923-0.984) calculated for the fungal populations of the Carpathian Basin. This may have resulted from the multiple introductions from diverse origins of the populations, close to the first site of observation in Northern Italy. The BAPS analysis of the microsatellite markers occasionally grouped together samples from remote geographical origin, suggesting human assistance in the introduction of new C. parasitica haplotypes from distinct areas.

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Diversity of Cryphonectria parasitica populations from the Carpathian Basin

The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasite, and
saprophyte fungal species. The currently applied classification is based on morphological characters.
In this study, a preliminary classification for six taxa of Phoma were constructed, viz. P. exigua var.
linicola, P. pinodella, P. eupyrena, P. herbarum, P. foveata, and P. destructiva, based on DNA
sequence data of translation elongation factor1 subunit (EF1 = tef1). The six Phoma species were
compared to two species of the closely related Ascochyta genus, and was divided into two clades. The
phylogenetic tree based on tef1 sequences does not support the traditional Phoma sections set up by
morphological characters.

Laszlo Irinyi

Papers

Phomas - can these fungi be used as biocontrol agents and sources of secondary metabolites? (A review).

Diversity of Cryphonectria parasitica populations from the Carpathian Basin

Classification of Phoma species using new phylogenetic marker

Szóján előforduló Phoma-szerű gombák filogenetikai vizsgálata Bayesian módszerrel

Morphology and molecular biology of Phoma