| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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In: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
-
Journal article (peer-reviewed)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
-
In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
-
Journal article (peer-reviewed)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.
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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
- 2015
-
In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
-
Journal article (peer-reviewed)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.
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| 4. |
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| 5. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
-
Journal article (peer-reviewed)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 6. |
- Abarenkov, Kessy, et al.
(author)
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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
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
-
Journal article (peer-reviewed)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).
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| 7. |
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| 8. |
- Hyde, Kevin D., et al.
(author)
-
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
- 2013
-
In: Current Research in Environmental and Applied Mycology. - : Mushroom Research Foundation. - 2229-2225. ; 3:1
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Journal article (peer-reviewed)abstract
- The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.
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| 9. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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An open source chimera checker for the fungal ITS region
- 2010
-
In: Molecular Ecology Resources. - : Wiley. - 1755-0998 .- 1755-098X. ; 10:6, s. 1076-1081
-
Journal article (peer-reviewed)abstract
- The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at http://www.emerencia.org/chimerachecker.html) to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.
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| 10. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
-
Journal article (peer-reviewed)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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| 11. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Improving ITS sequence data for identification of plant pathogenic fungi
- 2014
-
In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
-
Journal article (peer-reviewed)abstract
- Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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| 12. |
- Alm Rosenblad, Magnus, 1957, et al.
(author)
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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
- 2016
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 13, s. 21-33
-
Journal article (peer-reviewed)abstract
- During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
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| 13. |
- Hallenberg, Nils, 1947, et al.
(author)
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Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
- 2008
-
In: Botany. - 1916-2804. ; 86:11, s. 1319-1325
-
Journal article (peer-reviewed)abstract
- The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.). Key words: Polyporales, Radulodon, phylogeny, plant interactions. Résumé: Le Pseudolagarobasidium (Polyporales, Basidiomycota) constitue un genre de petits champignons résupinés qui comporte actuellement cinq espèces, toutes décrites à partir de régions tropicales ou subtropicales, incluant deux espèces parasites des racines d'arbres de la famille des légumineuses. On en a récemment établi la synonymie avec le genre Radulodon sur la base morphologique, mais les auteurs utilisent ici l'approche moléculaire. On constate que le genre Pseudolagarobasidium constitue un groupe monophylétique robuste excluant les Radulodon ce qui conduit au rejet de cette synonymie. L'amplitude écologique du genre va du saprophytisme au parasitisme, et on présente des preuves qu'au moins une lignée est un endophyte du cacaoyer (Theobroma cacao L.). Mots-clés : Polyporales, Radulon, phylogénie, interactions végétales.
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| 14. |
- Hyde, K. D., et al.
(author)
-
Global consortium for the classification of fungi and fungus-like taxa
- 2023
-
In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 15. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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A software pipeline for processing and identification of fungal ITS sequences
- 2009
-
In: Source Code for Biology and Medicine. - 1751-0473. ; 4:1
-
Journal article (peer-reviewed)abstract
- Background Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. Results The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50 % of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10 % of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. Conclusions The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
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| 16. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Approaching the taxonomic affiliation of unidentified sequences in public databases an example from the mycorrhizal fungi
- 2005
-
In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 6:178
-
Journal article (peer-reviewed)abstract
- Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service http://emerencia.math.chalmers.se webcite, users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets.
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| 17. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
- 2008
-
In: Evolutionary Bioinformatics. - 1176-9343. ; 2008:4, s. 193-201
-
Journal article (peer-reviewed)abstract
- The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequencebased mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3 % threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITSbased species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
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| 18. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
- 2017
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 26, s. 13-24
-
Journal article (peer-reviewed)abstract
- DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.
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| 19. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Rethinking taxon sampling in the light of environmental sequencing
- 2011
-
In: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 27:2, s. 197-203
-
Journal article (peer-reviewed)abstract
- Environmental DNA sequencing efforts of substrates such as soil, wood, and seawater have been found to present very different views of the underlying biological communities compared with efforts based on morphological examination and culture studies. The taxonomic affiliation of many of these environmental sequences cannot be settled with certainty due to the lack of proximate reference sequences in the corpus of public sequence data, and they are typically submitted to the international sequence databases without much indication of their relatedness. The scientific community has proved reluctant to include such unnamed sequences in phylogenetic analyses and taxonomic studies, but the present study shows such a position to be not only largely unwarranted but also potentially unsound. The sequences of 48 published fungal alignments of the nuclear ribosomal internal transcribed spacer region were subjected to similarity searches in the sequence databases to recover environmental sequences with a clear bearing on the respective ingroup. An average of 20 environmental sequences were added to each alignment, and upon rerunning the phylogenetic analyses of each study we found that topological rearrangements involving the original ingroup sequences were observed for no less than 29 (60%) of the studies. In nearly 20% of these cases, the rearrangements were large enough to question or even overthrow at least one conclusion presented in the original studies. The basal branching order was similarly subject to changes in 16% of the applicable studies. Environmental sequences are thus not only relevant in ecological research but form a requisite source of information also in systematics and taxonomy.
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| 20. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective
- 2006
-
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 1:1
-
Journal article (peer-reviewed)abstract
- Background DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. Methodology/Principal Findings The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. Conclusions The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.
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| 21. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
- 2009
-
In: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 296:1, s. 97-101
-
Journal article (peer-reviewed)abstract
- The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.
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| 22. |
- Nilsson, R. Henrik, 1976, et al.
(author)
-
Top 50 most wanted fungi
- 2016
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
-
Journal article (peer-reviewed)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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| 23. |
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| 24. |
- Ryberg, Martin, 1976, et al.
(author)
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An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity
- 2009
-
In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 181:2, s. 471-477
-
Journal article (peer-reviewed)abstract
- The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using BLAST. The results are made available as a biweekly updated web service that can be queried to retrieve all insufficiently identified sequences (IIS) associated with any fungal genus. The most commonly available annotation items in GenBank are isolation source (55%); country of origin (50%); and specific host (38%). The molecular sampling of fungi shows a bias towards North America, Europe, China, and Japan whereas vast geographical areas remain effectively unexplored. Mycorrhizal and parasitic genera are on average associated with more IIS than are saprophytic taxa. Glomus, Alternaria, and Tomentella are the genera represented by the highest number of insufficiently identified ITS sequences in GenBank. The web service presented (http://andromeda.botany.gu.se/emerencia.html#genus_search) offers new means, particularly for mycorrhizal and plant pathogenic fungi, to examine the IIS in GenBank in a taxon-oriented framework and to explore their metadata in an easily accessible and time-efficient manner.
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| 25. |
- Ryberg, Martin, 1976, et al.
(author)
-
DivBayes and SubT: exploring species diversification using Bayesian statistics
- 2011
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 27:17, s. 2439-2440
-
Journal article (peer-reviewed)abstract
- DivBayes is a program to estimate diversification rates from species richness and ages of a set of clades. SubT estimates diversification rates from node heights within a clade. Both programs implement Bayesian statistics and provide the ability to account for uncertainty in the ages of taxa in the underlying data, an improvement over more commonly used maximum likelihood methods.
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| 26. |
- Ryberg, Martin, 1976, et al.
(author)
-
Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)
- 2008
-
In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:50
-
Journal article (peer-reviewed)abstract
- Background The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera. Results Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusions Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.
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| 27. |
- Ryberg, Martin, 1976, et al.
(author)
-
New Ph.D. students in the empirical sciences should be recruited into ongoing scientific studies right from the start
- 2016
-
In: Journal of Brief Ideas.
-
Journal article (other academic/artistic)abstract
- All too often we come across Ph.D. students who after 2-3 years of effort still struggle with their first (co-)authorship. In many cases, this may be considered a waste of financial resources and human potential. We’d like to pitch the idea that newly started Ph.D. students should be invited to an ongoing study – thesis material or not – within the first weeks of their employment. The study should ideally be close to completion, and the task assigned to the Ph.D. student should comprise perhaps 2-3 days of work (plus manuscript revision). We have employed this approach many times, and the results so far have been encouraging: the Ph.D. students get a dose of positive energy from being part of a successful scientific enterprise and publication; they gets to feel that they and their work are taken seriously; and they obtain a quantum of experience of the scientific process. Furthermore, an early introduction to the notion of collaborative research efforts – a routine practice in academia and industry these days – is accomplished. This approach means little extra work for the project PI, but what strikes us is how long-lasting the positive effects for the Ph.D. students seem to be.
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| 28. |
- Tedersoo, Leho, et al.
(author)
-
Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of ITS sequences of mycorrhizal fungi
- 2011
-
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9
-
Journal article (peer-reviewed)abstract
- Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.
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| 29. |
- Durkin, Louisa, et al.
(author)
-
When mycologists describe new species, not all relevant information is provided (clearly enough).
- 2020
-
In: MycoKeys. - 1314-4049. ; 72, s. 109-128
-
Journal article (peer-reviewed)abstract
- Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years' worth (2009-2018) of species descriptions of extant fungal taxa - 1,097 studies describing at most ten new species - in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal species descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions - be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures.
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| 30. |
- Larsson, Ellen, 1961, et al.
(author)
-
Taxonomy and evolutionary relationships within species of section Rimosae (Inocybe) based on ITS, LSU and mtSSU sequence data
- 2009
-
In: Persoonia. ; 23, s. 86-98
-
Journal article (peer-reviewed)abstract
- The present study aimed at elucidating the structure of Inocybe subg. Inosperma sect. Rimosae but included also representatives from subg. Mallocybe and the genus Auritella. Phylogenetic relationships were inferred using ITS, LSU and mtSSU sequence data. The analyses recovered the ingroup as a monophyletic, strongly supported clade. The results indicate that recognizing Auritella on the genus level renders Inocybe paraphyletic. The species traditionally placed in sect. Rimosae were found to be distributed over two strongly supported clades, Maculata and Rimosae s.s. The Maculata clade clusters with sect. Cervicolores and the two represent subg. Inosperma in a strict sense. Rimosae s.s. emerges as an independent, supported clade well separated from Inosperma s.s. Twenty-one terminal groups were correlated with morphologically distinct species. In addition several taxa on single branches and minor less supported clades were recovered. A key to the identified species of the Maculata and Rimosae s.s. clades which occur in Northwest Europe is provided.
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| 31. |
- Leif, Örstadius, et al.
(author)
-
Molecular phylogenetics and taxonomy in Psathytellaceae (Agaricales) with focus on psathyrelloid species: introduction of three new genera and 18 new species.
- 2015
-
In: Mycological progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 14:5
-
Journal article (peer-reviewed)abstract
- Based on traditional morphology, sequence data,and phylogenetic analyses, 18 new species are here described: Coprinellus christianopolitanus, Coprinopsis musae, C. udicola, Psathyrel l a arenosa, P. carmine i ,P. fennoscandica, P. ichnusae, P. lilliputana, P. lyckebodensis, P. madida, P. rybergii, P. sabuletorum, P. scanica, P. siccophila, P. stridvallii, P. sublatispora, P. vesterholtii, and Typhrasa nanispora. Psathyrella hololanigera and P. tenera are reported as new to Europe and P. parva as new to the Nordic countries. A four-gene dataset on Psathyrellaceae were analyzed by Maximum Parsimony, Maximum Likelihood, and Bayesian methods. Constraint analyses were performed to determine limits of /Psathyrella, and to evaluate whether the / Coprinellus, /cordisporus, and /gossypina clades could be regarded with confidence as monophyletic clades outside of the clade /Psathyrella. This was not unambiguously supported. Based on the phylogenetic results, Kauffmania is proposed as a monotypic genus for the species P. larga and Typhrasa for P. gossypina and the new described species T. nanispora. The genus Homophron is formally validated and three combinations are proposed: H. spadiceum, H. cernuum, and H. camptopodum. The genus Cystoagaricus Singer is emended and the following new combinations are proposed: C. hirtosquamulosus, C. squarrosiceps, C. olivaceogriseus, and C. silvestris. Neotypes have been selected for seven species described by Fries, and ITS sequence data for these were generated. The following new combinations are proposed: Coprinopsis canoceps, C. cineraria, C. melanthina, C. submicrospora, C. uliginicola, and Typhrasa gossypina. Brief comments are given to other species of interest. Psathyrella ornatispora were found not to belong in Psathyrellaceae. A key to 106 psathyrelloid species in Northern Europe is provided.
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| 32. |
- Nordén, Björn, 1965, et al.
(author)
-
Dead wood in semi-natural temperate broadleaved woodland: contribution of coarse and fine dead wood, attached dead wood and stumps
- 2004
-
In: Forest Ecology and Management. - : Elsevier BV. - 0378-1127. ; 194:1-3, s. 235-248
-
Journal article (peer-reviewed)abstract
- Dead wood is essential for biodiversity in forests and is therefore often surveyed in conservation inventories. Usually only coarse downed trees (logs) and standing dead trees (snags) are surveyed, but dead wood also occurs on living trees, in stumps, and in fallen branches. Attached, standing (including stumps) and downed dead wood with a diameter of more than I cm was surveyed in 25 semi-natural stands of temperate broadleaved woodland dominated by oak in southern Sweden (most trees younger than 70 years but with an older generation of Quercus, and often Corylus scrub). This study is primarily motivated by the rising interest in biofuel harvesting by thinning which will affect dead wood structure in forests, especially the finer dead wood fractions. The sites in this study contained on average 14.3 m(3)/ha coarse dead wood (defined as wood with a diameter >10 cm), which is more than twice as much as in production woodland. Fine dead wood (diameter 1-10 cm) made up another 12.2 m(3)/ha (45% of the total dead wood volume). Of the fine dead wood, on average 20% was oak wood and 71 % was wood from other broadleaved trees. The coarse dead wood fraction consisted equally of oak wood (46%) and wood from other broadleaved species (47%). Coniferous wood amounted to 7% (coarse dead wood) or 8% (fine dead wood). The total dead wood volume was dominated by downed (66%) and standing dead wood (22%), while attached dead wood and stumps amounted to smaller fractions (6% each). The total volume of fine dead wood did not correlate with the total volume of coarse dead wood. These results therefore suggest that fine dead wood cannot be predicted from conservation surveys of coarse dead wood. The value for biodiversity of fine dead wood is discussed, and should not be overlooked in conservation work due to the fact that for example, many fungi and insects are associated with it. (C) 2004 Elsevier B.V. All rights reserved.
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| 33. |
- Nordén, Björn, 1965, et al.
(author)
-
Partial cutting reduces species richness of fungi on woody debris in oak-rich forests
- 2008
-
In: Canadian Journal of Forest Research. ; 38, s. 1807-1816
-
Journal article (peer-reviewed)abstract
- Partial cutting is increasingly applied in European temperate oak-dominated forests for biofuel harvesting, and to counteract succession in protected stands. Effects on biodiversity of these measures need to be carefully evaluated, and species-rich but neglected taxa such as fungi should be considered. We studied the effects of partial Cutting on fungal fruiting bodies on woody debris. In 21 closed canopy forests rich in large oaks in Sweden, on average 25%-30% of the basal area was cut. Fruiting bodies were counted and some were collected in treated and control plots before and after treatment. We found 334 basidiomycete and 47 ascomycete species. Species richness of basidiomycetes declined significantly more in treated plots (on average 26%) than in control plots (on average 13%) between seasons. Species richness of ascomycetes increased by 17% in control plots and decreased by 2% in treated plots. Total species richness was significantly reduced on fine woody debris (1-10 cm in diameter), but not on coarse woody debris (> 10 cm). Overall species composition did not change significantly as a result of partial cutting, but red-listed species tended to decrease more in treated plots. We suggest that approximately 30% of the stands should not be thinned, and dead sterns and fallen branches should not be removed, to favor saproxylic fungi and their associated fauna.
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| 34. |
- Nordén, Björn, 1965, et al.
(author)
-
Relative importance of coarse and fine woody debris for the diversity of wood-inhabiting fungi in temperate broadleaf forests
- 2004
-
In: Biological Conservation. - 0006-3207. ; 117:1, s. 1-10
-
Journal article (peer-reviewed)abstract
- Dead wood is considered important in forest conservation, but patterns of fungal diversity on dead wood have rarely been quantified. We investigated the relative importance of coarse (diameter > 10 cm) and fine woody debris (1-10 cm) for fungi in broadleaf forests in southern Sweden. The numbers of species per unit wood volume and per forest area were significantly higher for fine than for coarse woody debris for both ascomycetes and basidiomycetes. When the number of species was plotted against the number of records, coarse woody debris was more species rich than fine woody debris for a given number of basidiomycete records. Of the ascomycetes. 75% were found exclusively on fine woody debris (the corresponding proportion for basidiomycetes is 30%), 2% Were found exclusively on coarse woody debris (basidiomycetes 26%, and 23%,) of the species were found on both diameter classes (basidiomycetes 44%). We conclude that fine woody debris is important for diversity of wood-inhabiting fungi, especially ascomycctes. in this forest type. However, coarse woody debris must also be provided to insure the occurrence of many species of basidiomycetes. (C) 2003 Elsevier Ltd. All rights reserved.
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| 35. |
- Polme, S., et al.
(author)
-
FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
-
In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
-
Journal article (peer-reviewed)abstract
- 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.
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| 36. |
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| 37. |
- Ryberg, Martin, 1976, et al.
(author)
-
An evolutionary perspective on morphology and ecological characters in the mushroom family Inocybaceae (Agaricomycotina, Fungi)
- 2010
-
In: Molecular Phylogenetics and Evolution. - 1055-7903. ; 55:2, s. 431-442
-
Journal article (peer-reviewed)abstract
- Inocybaceae is one of the larger families among the gilled mushrooms (Agaricales) but their morphologybased taxonomy is still not fully settled considering molecular-based phylogenetic insights. Here we investigate the evolution of five morphological and four ecological characters using ancestral state reconstruction methods. All the morphological characters are correlated with the phylogeny, but we find spore shape and presence of cortina, to have the greatest taxonomic potential, as they are the most evolutionarily conserved. None of the five characters have, however, evolved in a way that easily delimits inclusive monophyletic groups and the section level taxonomy needs revision. Host preference, preference for calcareous soil, and soil nutritional status preference are shown to be reflective of the evolutionary history of the species at the scale investigated here while soil moisture preference is not. The states of three of the four ecological characters can therefore be predicted in a phylogenetic framework for species where they are unknown.
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| 38. |
- Ryberg, Martin, 1976
(author)
-
An evolutionary view of the taxonomy and ecology of Inocybe (Agaricales) with new perspectives gleaned from GenBank metadata
- 2009
-
Doctoral thesis (other academic/artistic)abstract
- Inocybe (Inocybaceae) is one of the most speciose genera among the gilled mushrooms (Agaricales) but large parts of its taxonomy and evolutionary history remain poorly explored. The present thesis sho... merws that the traditional infrageneric classification of Inocybe does not fully reflect evolutionary relationships and that the two most commonly used taxonomic characters, spore shape and presence of a cortina, have not evolved in such a way as to define unique monophyletic groups. The section Rimosae, in its traditional circumscription, is divided into two separate clades by the present analyses, and Rimosae s.str. does not group with the subgenus Inosperma - where it is commonly placed - but forms a separate clade more closely related to the subgenus Inocybe. Also the sections of the subgenus Inocybe, the largest of the subgenera, should in general be interpreted in a strict sense if they are to reflect monophyletic groups. Such a view-point would leave many species with an uncertain placement. On the species level it is shown that many of the traditionally accepted taxa are insufficiently characterized in terms of circumscription and morphological variation. This thesis also explores metadata associated with DNA sequences from molecular ecological studies. These sequences represent a large part of the fungal internal transcribed spacer (ITS) sequences in GenBank that are relatively well annotated regarding ecological and geographical data. They are, however, seldom used as sources of such information. One reason is that they typically lack precise taxonomic annotation and therefore are hard to search in a systematic context. To facilitate the exploration of such sequences, the software suite emerencia (www.emerencia.org) was developed and is presented as a component of this thesis. The emerencia software was employed to explore the distribution and ecology of Inocybe and was found to have the capacity to significantly expand on our knowledge of the world-wide distribution of the genus and of the ecology of its individual species. This new information was compiled together with information from other sources to explore whether host preference and three characters coding for preference for particular soil conditions are correlated to the phylogeny. This was done using ancestral state reconstruction methods. The results show that while soil moisture preference is not, host preference, preference for calcareous soils, and preference in soil nutritional status are indeed correlated to the phylogeny. This indicates that a well formulated taxonomy that is reflective of phylogenetic relationships can have predictive values for these ecological traits.
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| 39. |
- Ryberg, Martin, 1976, et al.
(author)
-
Ectomycorrhizal Diversity on Dryas octopetala and Salix reticulata in an Alpine Cliff Ecosystem
- 2009
-
In: Arctic, Antarctic, and Alpine Research. - : Informa UK Limited. - 1523-0430 .- 1938-4246. ; 41:4, s. 506-514
-
Journal article (peer-reviewed)abstract
- The ectomycorrhizal communities in alpine habitats have been relatively little studied. As global change is predicted to have a large impact in Arctic and alpine environments, it is important to document the fungi of these climatic regions to monitor changes and to understand upcoming successions. This study investigates the ectomycorrhizal community of Dryas octopetala and Salix reticulata on cliff ledges in a mid-alpine setting using the internal transcribed spacer region of nuclear ribosomal DNA for the identification of the fungal component of ectomycorrhizal root tips. It is shown that the community is relatively species rich, with 74 molecular operational taxonomic units (MOTUs)/species, and that it is dominated by Cenococcum geophilum, Thelephoraceae spp., Cortinarius spp., and Sebacinales spp. Furthermore, the dominating species have low specificity regarding the tested hosts and seem likely to be able to facilitate the succession of the alpine tundra to subalpine forest by serving as mycorrhizal partners for establishing pioneer trees.
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| 40. |
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| 41. |
- Ryberg, Martin, et al.
(author)
-
New light on names and naming of dark taxa
- 2018
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :30, s. 31-39
-
Journal article (peer-reviewed)abstract
- A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.
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| 42. |
- Ryberg, Martin, 1976, et al.
(author)
-
Weak habitat specificity in ectomycorrhizal communities associated with Salix herbacea and Salix polaris in alpine tundra
- 2011
-
In: Mycorrhiza. - : Springer Science and Business Media LLC. ; 21:4, s. 289-96
-
Journal article (peer-reviewed)abstract
- This study explores mid-alpine ectomycorrhizal communities on Salix herbacea and Salix polaris in plant communities differing in nutrient status and snow conditions. Plant species were identified by tracking roots back to above ground structures while fungal species were identified using molecular methods. The fungi were identified to 34 molecular operational taxonomic units (MOTUs)/species but species accumulation curves indicated that the communities were only partially sampled. The estimated total species richness was 49 (±9 SD) MOTUs/ species. No significant ectomycorrhizal community specificity was found between the two plant species and only weak specificity between different plant communities. Furthermore, no difference in proportion of colonized root tips could be demonstrated between plant communities. However, some fungal taxa showed tendencies to associate with specific environmental conditions. Sebacinaceae, Inocybe egenula, Russula cf.emetica, and a Tomentella sp. were found in meadow communities but not in the heath communities. Sistotrema cf. alboluteum and Tomentella cf. terrestris were only found in the dry and mesic heath communities. Classifications into exploration types showedthat the contact type is more abundant in the dry heath community than the other communities. Cenococcum geophilum was the most common species but Cortinarius spp., Russula spp., Tomentella spp., and Lactarius spp. were also common. This study confirms that alpine communities are rich in ectomycorrhizal fungi including species from a wide variety of fungal lineages and also show that many dominant species have wide ecological amplitude.
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