Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

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 using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

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 using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

MycoBank gearing up for new horizons

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 plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

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 using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Role of nutrient supply in yield increase and quality improvement of spice pepper

Hungarian spice pepper powder is a unique product, a real hungaricum with its flavour and aroma compounds and seasoning effect. Its competitiveness with foreign spice peppers is ensured by its high biological value deriving from the specially Hungarian production and processing technology. Besides the traditional and highly manual labour intensive processing technology, there are some modern industrial technologies as well, where high quality can be guaranteed only by producing excellent base material (raw pepper pods). This is the reason which necessitates the rational development of the elements of the production technology, such as nutrient supply. Our objective was to offer a contribution to this aim by our trials in plant nutrition. Experiments on the nutrient supply of spice pepper were set up in the 2003 growing season in order to decide whether yields and fruit composition parameters of pepper could be increased by means of increased K fertiliser doses with lower N:K ratios. Several forms of potassium were used, as well as applying microelement top dressings in the single treatments. It was found that the increase of N:K ratio from I:1 to 1:6 did not increase yields, but resulted in higher pigment and dry matter content. Microelement top dressing had a yield increasing effect at each N:K ratio. Higher potassium doses did not accelerate ripening

The effect of potassium fertilization on the inner values of spice pepper

To reserve the fertility of soil is the basic condition of successful cultivation. The field specific nutrient supply, based on soil tests is very important in both economy and ecology aspects. Spice pepper plants have high nutrient demands. Proper nutrient supply has importance not only from the point of potential yield levels, but make a major contribution to quality. This is the reason which necessitates the rational development of nutrient supply as an the elements of the production technology. Our objective was to offer a contribution to this job through our nutrient trials. Experiments on the nutrient supply of spice pepper were set up in the 2005 growing season in order to decide whether yields and fruit composition parameters of pepper could be increased by means of increased K fertiliser closes with lower N:K ratios. Several forms of potassium were used, as well as applying microelement top dressings in the single treatments. It was found that higher K doses lead to increased yields, and the influence on dry matter and pigment content proved beneficial too. Potassium applied in the form of patentkali seemed to be better than in that of potassium-sulphate

The effect of potassium fertilization on the inner values of spice pepper

To reserve the fertility of soil is the basic condition of successful cultivation. The field specific nutrient supply, based on soil tests is very important in both economy and ecology aspects. Spice pepper plants have high nutrient demands. Proper nutrient supply has importance not only from the point of potential yield levels, but make a major contribution to quality. This is the reason which necessitates the rational development of nutrient supply as an the elements of the production technology. Our objective was to offer a contribution to this job through our nutrient trials. Experiments on the nutrient supply of spice pepper were set up in the 2005 growing season in order to decide whether yields and fruit composition parameters of pepper could be increased by means of increased K fertiliser closes with lower N:K ratios. Several forms of potassium were used, as well as applying microelement top dressings in the single treatments. It was found that higher K doses lead to increased yields, and the influence on dry matter and pigment content proved beneficial too. Potassium applied in the form of patentkali seemed to be better than in that of potassium-sulphate

The effect of soil mixtures of different consistence and phosphorus content in tray transplant-growing by lettuce

The transplant-growing with root balls gets more and more popular and time to time the only method even in high-quality lettuce transplant-growing. To work out the technology of transplant-growing in trays it was needed to define the accurate physical and chemical consistency of applied soils. The transplant production in trays could become a good method in field-grown lettuce technologies. The production of transplants of good quality with this technology could be realised only by accurate soil mixtures. The matter of transplant-growing substrates could be a low-moor turf. Its qualities could be positively influenced by adding minerals like bentonite in amount of 5 (or 10) V%. To ensure enough phosphorus for the demands of transplants we have to add more fertilisers. The best results by lettuce we got by adding 4 kg/m3 superphosphate to the soil mixture