226 research outputs found
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
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.Comment: Submitted to Current Research in Environmental and Applied Mycology -
comments most welcom
Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
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.RHN acknowledges financial support from FORMAS (215-2011-
498) and from Stiftelsen Olle Engkvist Byggmästare. MPM was partially supported
by Plan Nacional I+D+i project CGL2012-35559. CW acknowledges a Marie
Skłodowska-Curie post doc grant (660122, CRYPTRANS)Peer reviewe
The curse of the uncultured fungus
The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked
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
Ionic structure and photoabsorption in medium sized sodium clusters
We present ground-state configurations and photoabsorption spectra of Na-7+,
Na-27+ and Na-41+. Both the ionic structure and the photoabsorption spectra of
medium-size sodium clusters beyond Na-20 have been calculated self-consistently
with a nonspherical treatment of the valence electrons in density functional
theory. We use a local pseudopotential that has been adjusted to experimental
bulk properties and the atomic 3s level of sodium. Our studies have shown that
both the ionic structure of the ground state and the positions of the plasmon
resonances depend sensitively on the pseudopotential used in the calculation,
which stresses the importance of its consistent use in both steps.Comment: 4 pages, 3 figures. Accepted for publication in PRB, tentatively July
15th, 1998 some typos corrected, brought to nicer forma
Revealing natural relationships among arbuscular mycorrhizal fungi: culture line BEG47 represents Diversispora epigaea, not Glomus versiforme
Background: Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified.
Methodology/Principal Findings:
Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as ‘G. versiforme BEG47’. We show by morphological comparisons, based on type material, collected 1860–61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora.
Conclusions: This study highlights that experimental works published during the last >25 years on an AMF named ‘G. versiforme’ or ‘BEG47’ refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF ‘laboratory strains’. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description
Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
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
Ionic and electronic structure of sodium clusters up to N=59
We determined the ionic and electronic structure of sodium clusters with even
electron numbers and 2 to 59 atoms in axially averaged and three-dimensional
density functional calculations. A local, phenomenological pseudopotential that
reproduces important bulk and atomic properties and facilitates structure
calculations has been developed. Photoabsorption spectra have been calculated
for , , and to
. The consistent inclusion of ionic structure considerably
improves agreement with experiment. An icosahedral growth pattern is observed
for to . This finding is supported by
photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality
can be requested from the author
Tree diversity and species identity effects on soil fungi, protists and animals are context dependent
Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se
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