| 1. |
- Abarenkov, Kessy, et al.
(författare)
-
Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
-
Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
-
Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
|
|
| 2. |
- Hibbett, David, et al.
(författare)
-
Sequence-based classification and identification of Fungi
- 2016
-
Ingår i: Mycologia. - 0027-5514. ; 108:6, s. 1049-1068
-
Forskningsöversikt (refereegranskat)abstract
- 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 understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
|
|
| 3. |
- Kõljalg, Urmas, et al.
(författare)
-
Digital identifiers for fungal species
- 2016
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 352:6290, s. 1182-1183
-
Tidskriftsartikel (refereegranskat)
|
|
| 4. |
- Koureas, Dimitrios, et al.
(författare)
-
Unifying European Biodiversity Informatics (Bio Unify)
- 2016
-
Ingår i: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 2:e7787, s. 1-23
-
Tidskriftsartikel (refereegranskat)abstract
- In order to preserve the variety of life on Earth, we must understand it better. Biodiversity research is at a pivotal point with research projects generating data at an ever increasing rate. Structuring, aggregating, linking and processing these data in a meaningful way is a major challenge. The systematic application of information management and engineering technologies in the study of biodiversity (biodiversity informatics) help transform data to knowledge. However, concerted action is required to be taken by existing e-infrastructures to develop and adopt common standards, provisions for interoperability and avoid overlapping in functionality. This would result in the unification of the currently fragmented landscape that restricts European biodiversity research from reaching its full potential. The overarching goal of this COST Action is to coordinate existing research and capacity building efforts, through a bottom-up trans-disciplinary approach, by unifying biodiversity informatics communities across Europe in order to support the long-term vision of modelling biodiversity on earth. BioUnify will: 1. specify technical requirements, evaluate and improve models for efficient data and workflow storage, sharing and re-use, within and between different biodiversity communities; 2. mobilise taxonomic, ecological, genomic and biomonitoring data generated and curated by natural history collections, research networks and remote sensing sources in Europe; 3. leverage results of ongoing biodiversity informatics projects by identifying and developing functional synergies on individual, group and project level; 4. raise technical awareness and transfer skills between biodiversity researchers and information technologists; 5. formulate a viable roadmap for achieving the long-term goals for European biodiversity informatics, which ensures alignment with global activities and translates into efficient biodiversity policy.
|
|
| 5. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
-
Ingår i: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
-
Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
|
|
| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
Molecular techniques in mycological studies and sequence data curating: quality control and challenges
- 2016
-
Ingår i: Biology of Microfungi. - Switzerland : Springer International Publishing. - 9783319291352 ; , s. 47-64
-
Bokkapitel (refereegranskat)abstract
- Molecular (DNA sequence) data are a routine source of information in mycology. Environmental sequencing efforts of substrates, such as soil, wood, and air, have revealed vast numbers of previously unknown or poorly understood species, and their integration in the classification system of fungi and the fungal tree of life represent significant challenges. Underpinning such efforts are reference datasets of reliable sequences to which newly generated sequences can be compared for taxonomic affiliation and perhaps hints of species traits and ecological roles. The public sequence databases are however accumulating countless sequences that are compromised in terms of taxonomic annotation or technical quality. Metadata on, e.g., country or host of collection and any specimen/culture association are similarly lacking for the majority of entries. This invites further mistakes and reduces scientific explanatory power. This chapter discusses how to spot compromised sequences and what to do when they are found. These curation principles are implemented in the fungal nuclear ribosomal internal transcribed spacer (ITS) sequence database UNITE (http://unite.ut.ee) for molecular identification of fungi. UNITE supports web-based third-party sequence annotation, and the reader is invited to take part in the annotation effort.
|
|
| 7. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
- 2019
-
Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1
-
Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
|
|
| 8. |
- Oja, Jane, et al.
(författare)
-
Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands
- 2017
-
Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 27:4, s. 355-367
-
Tidskriftsartikel (refereegranskat)abstract
- Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.
|
|
| 9. |
- Ronquist, Fredrik, 1962-, et al.
(författare)
-
EU-BON Deliverable 1.3. Systems for mobilizing and managing collection-based data (specimen + DNA-data) fully integrated
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Introduction. A large portion of the biodiversity data in natural history collections is still not available digitally. Increasingly, innovative high-throughput methods are being applied to digitize this backlog in bulk, generating large amounts of data. In parallel, natural history museums are becoming increasingly involved in the generation of large amounts of molecular biodiversity data using new massively parallel sequencing platforms. Against this backdrop, the goal of EU BON Task 1.4 has been to support data mobilization efforts targeting collection-based and molecular data, mainly through the development and integration of innovative open-source tools and services.Progress towards objectives. The activities have involved work within the context of three major projects: i) DINA, an open-source, modular, web-based collection management system for natural history specimen data. ii) JACQ an open-access system for botanical (herbarium) data. iii) PlutoF, a web platform for working with traditional and molecular biodiversity research data. The task has also involved work on a number of other EU BON partner systems and services, as well as integration across internal EU BON and external biodiversity informatics resources. Finally, these systems have been used for targeted data mobilization efforts.Achievements and current status. Within DINA, the focus has been on supporting the engineering of sophisticated biodiversity information systems through the exploration of tools supporting distributed development and a modular plug-and-play design based on services-oriented architectures. This has involved the testing and adoption of tools like Apiary for the design of Application Programming Interfaces (APIs) and Docker for systems integration and deployment tasks. A Python library for data migration to DINA was also developed and tested. Within JACQ, a number of tools were developed to facilitate deployment and data migration to the system, and the AnnoSys tool for annotation of data has been integrated. Within PlutoF, EU BON efforts focused on the development of a citizen-science module and improved functionality for the mobilization of collection (living) specimen data. A number of innovative tools were developed by Pensoft to help mobilize biodiversity data published in the scientific literature, including semantic mark-up of species conservation papers, direct import of data from a range of biodiversity platforms into manuscripts, and a mechanism for providing stable links from publications to global biodiversity repositories. Plazi implemented an automated workflow mining published scientific papers for taxonomic data, currently mobilizing 25 % of all published new names as they become available. GlueCad developed apps allowing citizen scientists reporting spontaneous observations or systematic inventory data to select target taxa and preferred data mobilization platform. IBSAS and UCPH have focused on national data mobilization efforts targeting Slovakia and Denmark, respectively.Future developments. Although the development is clearly towards increased integration of biodiversity informatics tools into larger and more sophisticated systems, it is clear that there is no one size that fits all. Nevertheless, the increasingly widespread adoption of community standards, open-source development practises and service-oriented architectures are pushing the capability of current systems forward and facilitating tighter integration across systems. This trend is supported by the appearance of sophisticated tools enabling the design and deployment of complex modular systems. The adoption of the Docker approach is one example of how the biodiversity informatics community may benefit from this.
|
|
| 10. |
- Svantesson, Sten, et al.
(författare)
-
Solving the taxonomic identity of Pseudotomentella tristis s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data
- 2019
-
Ingår i: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 50, s. 1-77
-
Tidskriftsartikel (refereegranskat)abstract
- P. tristis is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to P. tristis, but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of P. tristis and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material. We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1 alpha and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database. We found the P. tristis group to contain 13 molecularly and morphologically distinct species. Three of these, P. tristis, P. umbrina and P. atrofusca, are already known to science, while ten species are here described as new: P. sciastra sp. nov., P. tristoides sp. nov., P. umbrinascens sp. nov., P. pinophila sp. nov., P. alnophila sp. nov., P. alobata sp. nov., P. pluriloba sp. nov., P. abundiloba sp. nov., P. rotundispora sp. nov. and P. media sp. nov. We discovered P. rhizopunctata and P. atrofusca to form a sister clade to all other species in P. tristis s.l. These two species, unlike all other species in the P. tristis complex, are dimitic. In this study, we designate epitypes for P. tristis, P. umbrina and Hypochnopsis fuscata and lectotypes for Auricularia phylacteris and Thelephora biennis. We show that the holotype of Hypochnus sitnensis and the lectotype of Hypochnopsis fuscata are conspecific with P. tristis, but in the absence of molecular information we regard Pseudotomentella longisterigmata and Hypochnus rhacodium as doubtful taxa due to their aberrant morphology. We confirm A. phylacteris, Tomentella biennis and Septobasidium arachnoideum as excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of the P. tristis group is provided. We found P. umbrina to be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in the P. tristis group were found to be less common and have narrower ecological niches.
|
|
